Schrödinger - Support - Knowledge Base


 OOPS 5: ipose = parentpose(        5001 ) =         5001 , iscreen =           1

 OOPS: ligrunsp before call convertcluopt1:          ipose=        5001

Article ID: 1036 - Why are there nonplanar aromatic rings in docked poses?

Article ID: 244 - Sometimes I find distorted phenol rings coming out of a Glide docking run. Why is that and how should I get rid of the distortion?

Article ID: 192 - How do I perform a conformational search on a set of ligands and constrain a substructure or torsion that is conserved in each input structure ?

Article ID: 1222 - Are there any training videos that demonstrate how to use KNIME ?

Article ID: 1725 - Maestro crashes or freezes my MacBook Pro. What can I do?

Article ID: 1729 - On my Mac, when I pick atoms in Maestro by dragging over them, the structure becomes blurred and moves a bit to the top left. Is there a way to fix this?

Article ID: 1751 - The online help doesn't seem to be working on my Mac. What can I do about it?

Article ID: 1749 - I started a job on my Mac, and logged out. When I logged back in again, the job had died. What is the problem?

Article ID: 1748 - Where can I obtain ligand databases for virtual screening?

Article ID: 1461 - How should I install Maestro Elements? Do I need to install Maestro as well?

Article ID: 867 - Is it possible to run IFD with a fixed ligand core, as in Glide docking?

Article ID: 700 - Is there a way to build with fragments that aren't in the Fragments tab of the Build panel?

Article ID: 1747 - How do I install a non-server-based (node-locked) license?

Article ID: 1744 - My Windows laptop is stereo-capable, so why doesn't it work with Maestro in stereo? I have an Nvidia graphics card.

Article ID: 1743 - Why does the Ligand Interaction Diagram (LID) fail with messages "Error: LID cannot render molecule" and "Exception: input molecule has more than 300 atoms, check input for valid protein-ligand complex"?

Article ID: 1742 - Can I export fasta sequences from structures in Maestro?

Article ID: 1741 - How can I use a different version of OPLS in my MM-GBSA jobs?

Article ID: 1734 - When I open the manuals index in Adobe Reader on Linux, the links to the manuals don't work. What's the problem?

Article ID: 1519 - How do I delete records from a Phase database for molecules that are defined in a structure file?

Article ID: 1516 - Is there a way to change the rendering of the H-bonds? I'd like to emphasize them a bit more.

Article ID: 1287 - How do I enable hardware stereo with my NVIDIA graphics card under Linux?

Article ID: 1286 - What stereo viewing methods are available in Maestro, and how do I access the stereo controls?

Article ID: 843 - Can I use the Zalman Trimon monitor for 3D display in Maestro? What requirements if any are there to display in stereo with this monitor?

Article ID: 546 - What is the correct reference for OPLS_2005? Is there any publication where we can find the OPLS_2005 parameters?

Article ID: 371 - How do I configure my Linux system to use a Zalman monitor for interlaced stereo with an Nvidia graphics card?

Article ID: 231 - I would like to share a KNIME workflow with my colleague. What is the best way to do that?

Article ID: 1739 - I cannot run the Chemistry External Tools on Windows. Is there a way to get this to work?

Article ID: 1738 - After installing the Suite 2012 Schrödinger KNIME extensions in my KNIME installation, I see an error message in the log,

ERROR RepositoryFactory CODING PROBLEM Icon 'src/com/schrodinger/knime/icons/schrodinger64.png' for category /schrodinger/cheminformatics/Modeling does not exist

Is this a problem, and what should I do?

Article ID: 1737 - Do I need to prepare molecules from the ZINC database for docking? If so, how should I download and prepare the structures?

Article ID: 1736 - When Glide constraints are applied during docking, is the energy from the restraining potentials included in the scoring?

Article ID: 1735 - Why does Maestro open the manuals index in KPDF rather than Adobe Reader?

Article ID: 1733 - When I upgrade to Suite 2012 Update 2 on my Windows machine from Suite 2012 or Suite 2012 Update 1, the upgrade fails for Prime and CombiGlide. What do I need to do to complete the upgrade?

Article ID: 870 - I saved my project with a new name. When I tried to open the new project, there was a warning message indicating the project is being cleaned and cannot be opened.

WARNING : MMPROJ WARNING(-3): mmproj_project_open():
The project project cannot be opened now.
It is being cleaned by process pid on host

How can I get my project to open?

Article ID: 1724 - I upgraded my Mac to OS X 10.8 Mountain Lion and now none of my Schrödinger apps work. What do I do?

Article ID: 1732 - Is there a way to import a structure by using its common name or its IUPAC name?

Article ID: 1659 - The links in the Suite 2012 Manuals Index appear to be messed up. What's the problem?

Article ID: 1731 - How do I set up a custom lambda schedule for Desmond FEP jobs?

Article ID: 1730 - I can't start the license server on my Windows machine. What's wrong?

Article ID: 1728 - When I run Desmond or Jaguar in parallel across multiple Macs, I see the following errors in the log file:

mca: base: component_find: "mca_plm_rsh.la" does not appear to be a valid plm MCA dynamic component (ignored): dlsym(0x10010b660, mca_plm_rsh.la_component): symbol not found

Is this serious?

Article ID: 1727 - Can I superimpose a trajectory on an external structure, and if so, how?

Article ID: 1726 - What is the difference between MMFF and MMFFs?

Article ID: 1723 - Currently, in loop refinement, residues within a certain distance of the loop residues are included in the refinement. Is it possible to supply a list of specific residues to include in the refinement, rather than using the distance option?

Article ID: 1721 - I see warning messages saying "Database index file filename could not be opened, and cannot open my Maestro project. What can I do?

Article ID: 1648 - Can I use Glide to score poses produced by Prime Covalent Docking?

Article ID: 1442 - I want to use web-based searching with Prime, but I have to go through a proxy server. How can I set this up?

Article ID: 1105 - How can I compare covalent docking results for multiple ligands?

Article ID: 1096 - My LigPrep job failed part way through. Is there any way that I can run the rest of the job?

Article ID: 955 - How can I remove duplicates from a set of ligand-like structures?

Article ID: 707 - What's the best way to filter out poses with bad torsions?

Article ID: 348 - What is the difference between the docking score and GlideScore from the results of a docking run?

Article ID: 1722 - When trying to launch a Glide Grid Generation job, I see a pop-up warning indicating that "The Workspace contains one or more unidentified ligand-sized molecules". What does this mean?

Article ID: 1356 - How can I install and use the Prime Threading pathway?

Article ID: 1711 - I'm getting no results when I try to search the online help on my Linux machine. What is the problem?

Article ID: 1720 - Why are there different SMARTS patterns for the members of a single MCS group?

Article ID: 972 - How do I set up access to the license server from a client machine?

Article ID: 1719 - Why does Maestro freeze on Windows when I try to export structures?

Article ID: 1278 - What structure file formats can be used with Maestro?

Article ID: 1457 - How can I optimize the performance of Maestro?

Article ID: 103 - Maestro is slow to launch and frequently crashes. What could the problem be?

Article ID: 1006 - How can I create a custom solvent model for Desmond simulations?

Article ID: 1718 - Some of the keyboard shortcuts don't work. What can I do about this?

Article ID: 1717 - When I open a Maestro panel, it doesn't show up on my screen. What happened, and is there anything I can do to display it on screen?

Article ID: 1606 - How do I make rsync_pdb and update_BLASTDB work with a proxy server using the web_proxy.json file, which I set up for getpdb? At present it fails with the error

rsync: failed to connect to prime.schrodinger.com: Network is unreachable (101)
rsync error: error in socket IO (code 10) at clientserver.c(124) [receiver=3.0.6]

Article ID: 1525 - I can't use rsync_pdb and update_BLASTDB on my Linux machine, because they don't get past our web proxy. Is there anything I can do to fix this?

Article ID: 1515 - When I generate a surface, I only want to see the portion that is in the active site. Is there a way of doing this?

Article ID: 383 - I downloaded the Maestro program through the Maestro Academic campaign and installed it on my computer. But I cannot do any energy minimization for the molecules I have drawn. What can I do?

Article ID: 373 - When I started Maestro remotely using the commands:

ssh user -X
$SCHRODINGER/maestro -SGL

I got the error:

Xlib: extension "SHAPE" missing on display "localhost:10.0".
X Error: BadMatch (invalid parameter attributes) 8
Extension: 139 (RENDER)
Minor opcode: 4 (RenderCreatePicture)
Resource id: 0x420041f

What's the "SHAPE" that is missing?

Article ID: 1716 - I have extracted a ligand from a PDB structure. How do I prepare the ligand for modeling, by adding multiple bonds, hydrogens, and generating reasonable ionization states?

Article ID: 1302 - I'm having problems with Workspace objects that are displayed poorly or incorrectly, are not displayed at all, or vanish. What can I do?

Article ID: 832 - On Windows, I'm seeing black horizontal stripes on the bonds in tube and ball-and-stick representation. How do I get rid of these?

Article ID: 1712 - When I try to search the online help, I get a message that the browser cannot connect to the server at localhost:9001. What does this mean, and what can I do about it?

Article ID: 908 - My KNIME node descriptions are not displaying properly. What can I do?

Article ID: 1713 - My Phase database search job dies with an error similar to:

terminate called after throwing an instance of 'std::bad_alloc'
what(): St9bad_alloc

What is the reason for this error and how can I get my search to run?

Article ID: 574 - Can I perform protein-protein docking with Schrodinger software?

Article ID: 1553 - I would like to execute a series of Maestro commands on multiple entries in the Maestro Project Table. Is there a way to do this?

Article ID: 1548 - Is it possible in Maestro to define macros and assign them to the Function (F) keys?

Article ID: 1546 - Is it possible to assign shortcut keys to specific menu options in Maestro?

Article ID: 1541 - I prefer to use the left mouse button to rotate structures in Maestro rather than the middle mouse button. Is there a way to remap the mouse buttons to make this possible?

Article ID: 441 - Can I label multiple entries in the Project Table with the stars?

Article ID: 1102 - Can I choose the PDF viewer that is used to view the documentation from Maestro?

Article ID: 871 - What does the following Maestro error message mean?

WARNING : MMDBI ERROR(-4): mmproj_dbi_db_open():
Failed to set the pragma
WARNING : MMPROJ ERROR(-4): mmproj_project_new():
failed to open the entryproperties database.
WARNING MM_DGOList::draw(void): Could not draw DGOList SurfaceMC, DGO SurfaceDGO

Article ID: 1581 - How do I use the Pose Viewing Mode in Maestro?

Article ID: 1542 - I see in the Protein Preparation Wizard (PPW) a button called "Interactive Optimizer". What does this do and how do I use the Interactive Optimizer?

Article ID: 1540 - How do I define a shell of restrained and frozen atoms in MacroModel?

Article ID: 1710 - I don't have a license for the Schrödinger extensions. Can I still read and write Maestro files, and start Maestro from KNIME?

Article ID: 1706 - How do I uninstall a Schrödinger suite from my Mac?

Article ID: 1485 - I would like to identify structural homologs in the PDB for a protein without any regard to sequence identify. Is there a way to do this with Schrödinger software?

Article ID: 1709 - Installation on Windows failed due to insufficient disk space, but I'm sure I have enough disk space for the installation. How can this happen?

Article ID: 1696 - How do I start KNIME from a standalone installation so the Schrödinger nodes can be run?

Article ID: 1451 - I can't start KNIME on Ubuntu 10.04.1. It tells me that my version of SQLite is too old. Is there anything I can do to get it working?

Article ID: 1708 - How can I get contributions to the GlideScore from particular receptor atoms or residues?

Article ID: 1707 - Why is Glide producing output poses that don't satisfy my constraints?

Article ID: 1705 - Why does my Jaguar geometry optimization job fail when using the SM8 solvent model?

Article ID: 1704 - When I add up energy terms in the Project Table from a Prime energy calculation job, the sum of the terms is not equal to the reported Prime Energy. Why is this?

Article ID: 1703 - I would like to export just the ligands from an Induced Fit docking output file. How do I do this?

Article ID: 1702 - Why do the BLAST search results differ between Simple Homology Modeling (and Residue Scanning) and the Advanced Homology Modeling?

Article ID: 1701 - In KNIME, when should I use the Run Maestro 1:1 metanode, and when should I use the KNIME-Maestro connector node?

Article ID: 1700 - Is there a quick way to visualize my antibody structure in BioLuminate?

Article ID: 1699 - How can I easily visualize my system's binding region in BioLuminate?

Article ID: 1698 - I have two interacting proteins and would like to visualize the interaction interface between them in BioLuminate. How do I do this?

Article ID: 1697 - What can I try if the software download is interrupted?

Article ID: 1588 - How do I generate a ray-traced image of the Maestro workspace using PyMOL?

Article ID: 1587 - Is there a way to edit the standard colors and color schemes in Maestro?

Article ID: 1586 - Is there a tutorial on examples of useful shortcut keys in Maestro?

Article ID: 1585 - How do I use the Views feature in Maestro and is there a way to make a movie from a series of saved views?

Article ID: 1584 - How do I use Scenes in Maestro to make and share presentations?

Article ID: 1583 - How do I use Find in the Maestro workspace and the Project Table?

Article ID: 1582 - Is there a way to filter ligands based on property values?

Article ID: 1580 - How do I rank a structure using stars and is there a way to mark structures in the Project Table as I view them in Maestro?

Article ID: 1579 - Is there a way to manually adjust in real time the conformation of a small molecule or protein in Maestro?

Article ID: 1578 - Is there a way in Maestro to add text annotations or captions to the 3D workspace? Also, is there a way to highlight certain atoms or residues?

Article ID: 1577 - How do I change the material and lighting effects of objects in the Maestro workspace?

Article ID: 1576 - Is there a tutorial on how to use Workspace Style in Maestro, which I understand can be used to automatically set molecular representation, and display of hydrogen bonds, waters, ribbons, etc?

Article ID: 1551 - How do I change the chirality of a molecule in Maestro?

Article ID: 1550 - I sometimes see yellow text in the upper left corner of the Maestro window. What is this text, how do I control the content of the text, and how do I turn the text on and off?

Article ID: 1549 - I see that in Maestro 9.2 (Suite 2011), there is a 2D sketcher. Is there a tutorial on how to use it?

Article ID: 1547 - How do Project Table Property Families work in Maestro 9.2 (Suite 2011)?

Article ID: 1545 - There are quite a few toolbars in Maestro (Suite 2011 and 2012). Is there a way to customize the location, style (e.g., display icon & text, icon only, or text only), and which buttons are displayed?

Article ID: 1544 - I've noticed in Maestro that there is a menu displayed when I right-click. Is there a tutorial on what can be done with this menu?

Article ID: 1543 - I would like to build a molecule in Maestro using the 3D Builder toolbars. What is the easiest way to learn how to do that?

Article ID: 1539 - When I view a ligand in the Maestro workspace, it's a little cluttered and hard to see the ligand. Is there a way to adjust the default clipping plane width to make views of ligands clearer.

Article ID: 652 - How does Glide use confgen during a docking simulation?

Article ID: 641 - Does Glide docking include a global conformation search?

Article ID: 467 - I want to calculate the surface area of a protein binding site, defined as any residue 6 Å from the ligand, and also the volume of the binding site. How do I do this?

Article ID: 1694 - Using the Schrödinger nodes in KNIME doesn't seem to work on Windows. What might be wrong?

Article ID: 1693 - When rotating a structure in Maestro on my Windows machine, there are short pauses in the rotation. Is there a way to fix this?

Article ID: 1512 - I can't open the online help from Maestro, and I see an error "Couldn't load XPCOM". Is there a fix for this problem?

Article ID: 1530 - Why do I see warnings about LSF in my Desmond and Jaguar log files?

Article ID: 328 - How do I display all formal charges on a small molecule complexed with a protein e.g, a -1 adjacent to the carboxylate O? How do I display the formal charge on all atoms that are not neutral in a molecule?

Article ID: 281 - I have problems with access to the Schrödinger software licenses. Is there an easy way to collect all the system configurations for technical support to help me?

Article ID: 214 - Can I create a pharmacophore hypothesis based only on my protein binding site, without having a native ligand?

Article ID: 1691 - When I try to view XP descriptors from Suite 2011 in the XP Visualizer in Suite 2012, I get an error message:

Unable to find required values in the input file

Is there a way around this problem?

Article ID: 1690 - When running a Glide Ligand Docking job with Schrodinger Suite 2012 (Maestro 9.3), the ligand titles in the output pose file are overwritten with the receptor title. Is there a way to fix this problem?

Article ID: 1689 - Is it possible to restart a Prime MM-GBSA job?

Article ID: 1688 - When I upgraded to Suite 2012, I found that I could no longer use rsh for remote job submission. Is it still supported?

Article ID: 1169 - What are the BuryP and Site scores in Glide jobname.rept and jobname.scor files? How do these relate to the GlideScore terms described in the Glide Technical Notes? What is Efinal in the jobname.log?

Article ID: 1687 - I would like to try out the new KNIME workflows menu in Maestro. Where can I look at a few examples?

Article ID: 730 - What does the internal energy include in the Glide docking results? Is it just the energy difference of the final pose and its minimized conformation?

Article ID: 1686 - Closing or opening a project takes a long time. Is there anything I can do about this?

Article ID: 1284 - How can I improve the drawing speed in Maestro?

Article ID: 1282 - Maestro is slow to rotate structures. Is there anything I can do?

Article ID: 1685 - How I can ensure that the corporate title present in my SD or Smiles input file for a virtual screening or Phase database generation is used as the title in the screening results or in the Phase database?

Article ID: 1684 - Is there a way to run a conformational search specifically for macrocycles?

Article ID: 1683 - What can I use the Select Top Poses script for?

Article ID: 1682 - What is the difference between Glide core RMSD as set up in the Core tab, and the feature "Compute RMSD to input ligand geometries" in the Output tab? Which should I use?

Article ID: 1681 - What is the difference between Core and Positional constraints? Which do I use if I want to positionally constrain the core of my molecule?

Article ID: 1680 - There don't seem to be any velocities in my Desmond trajectory. Why is this?

Article ID: 1679 - Why does my Glide or Impact job fail with an error that an atom has "too many bonds"?

Article ID: 1678 - How do I prepare and use a cofactor-containing receptor for Glide docking?

Article ID: 1034 - Do Glide docked poses depend on the initial ligand conformations?

Article ID: 382 - I have a license server, and I would like to run Maestro on a new, different Windows machine. How do I set up the license ?

Article ID: 1677 - How do I assign proper partial charges to my structures for Glide docking or other applications?

Article ID: 1650 - How can I visualize the grid boxes for an existing Glide grid?

Article ID: 511 - Do you support maegz format for all of the applications?

Article ID: 366 - How can I change the color of hydrogen bonds so as to be seen clearly on a white background?

Article ID: 361 - Is it possible to prepare a protein at a user-defined pH?

Article ID: 357 - Are alternate side-chain conformations considered when using the Protein Preparation Wizard?

Article ID: 347 - If I can't find common pharmacophores when developing a pharmacophore model in Phase, what is the best way forward with the options available to me?

Article ID: 201 - After doing the restrained minimization (impref) in the Protein Preparation Wizard, the metal ion often moves quite a lot from its original positions. What should I do to keep it restrained?

Article ID: 200 - I want to extract the ligand from the binding pocket. What is the fastest way to do that?

Article ID: 140 - How do I import structures to and from MOE?

Article ID: 130 - I would like to customize my .msj file for multisim. Where can I learn more about the file format and syntax?

Article ID: 6 - What's the best way of adding a disulfide bond between two cysteine residues in a protein structure?

Article ID: 1520 - Is it possible to calculate ligand desolvation energies with Prime MM-GBSA?

Article ID: 1474 - I can't run remote jobs. What should I do?

Article ID: 1427 - How can I perform a substructure search on Project Table entries in Maestro ?

Article ID: 1348 - Can I apply distance, angle, or dihedral constraints on the sites when searching for matches to a hypothesis?

Article ID: 1172 - How do I generate a Glide grid from a SiteMap binding site?

Article ID: 892 - I want to do a transition state search with Jaguar, but the atom numbering for my product and reactant entries is different, and I can't run the calculation. How do I change the atom numbering?

Article ID: 890 - Is there a way to transfer the Maestro Workspace into PyMOL?

Article ID: 884 - Maestro failed to start with the following error message. I have a license, so what can I do to fix this problem?

FATAL got_license: could not check out a license for mmlibs version 1.8
FATAL mmerr_initialize: got_license() failed
FATAL -15: Unable to obtain valid Maestro license key. MAESTRO_MAIN

Article ID: 766 - Can I use Glide grids from earlier releases with the current software? Or is there some conversion utility to "update" a set of grid files?

Article ID: 669 - Can I dock ligands with Glide so that the ligand forms a covalent bond with the receptor?

Article ID: 549 - Is there a way to add or modify OPLS parameters for metal coordination geometry?

Article ID: 414 - What is an easy way in Maestro to take snapshots of a selected rectangular area and save it in JPG, GIF, or TIF format? I want to use the image in a PowerPoint presentation and don't want the images to be too large.

Article ID: 351 - I've created a surface for my entry in the Workspace and only want to clip the surface, and leave the atoms (e.g., the ligand in my protein) intact (i.e., visible). Is that possible?

Article ID: 195 - Can I run KNIME workflows from the command line, without using the KNIME user interface ?

Article ID: 181 - I performed a calculation starting from the Maestro interface on Windows. After finishing I could not find the files the applications should have written out. What did I do wrong?

Article ID: 76 - While working in Maestro, I get error messages in the terminal like:

WARNING : MMDBI ERROR(-4): mmproj_dbi_clear_undo(): Failed to clear the undo tables (database is locked)
WARNING : MMPROJ ERROR(-4): local_mmproj_prepare_db_for_potential_undo(): Failed to clear the undo

What does this mean?

Article ID: 1590 - How can I use Unix-style commands or a Unix shell on Windows?

Article ID: 1575 - I liked the toolbar layout in Maestro 9.1 (Suite 2010), and I noticed that the toolbars changed in Maestro 9.2. Is it possible to revert the toolbar layout to that of Maestro 9.1?

Article ID: 1482 - I'm seeing nonplanar aromatic groups in my protein when I minimize with Prime. Is there a way to fix this?

Article ID: 1478 - Does Glide reward the interaction between a neutral acceptor atom of a ligand and a metal ion?

Article ID: 1475 - I'd like to use the loop prediction method that Rich Friesner described in a recent presentation in which he showed extremely accurate prediction of long loops (14-20 residues). Can I access this method using Prime?

Article ID: 1355 - How can I download the full Prime package?

Article ID: 1320 - How do I prevent the view in the clipping planes window from zooming in when I fit a selected residue to the screen?

Article ID: 1318 - Does Maestro provide any capabilities for shading structures?

Article ID: 1285 - Maestro is slow to respond. Is there anything I can do?

Article ID: 1251 - How do I run LigPrep from the command line?

Article ID: 1174 - When I run a Glide, QSite, Impact, or Liaison job with a large protein, I sometimes get an error that there are "too many atoms". What can I do?

Article ID: 1073 - Can I run a KNIME workflow from the command line on Windows?

Article ID: 1042 - Why is the metal-binding term zero when the ligand clearly interacts with the metal-containing part of the protein?

Article ID: 952 - Can I install new Schrödinger software in an existing Schrödinger directory?

Article ID: 927 - I would like to use Glide to dock to an RNA molecule that is rather large. How can I generate a grid for my target?

Article ID: 913 - In my Glide docking calculations, benzofuran was given a cis conformation, rather than trans. How can I get the correct conformation?

Article ID: 862 - How do I get Canvas to open PyMOL in Suite 2010?

Article ID: 737 - When using Glide, I got this message:

Disk quota exceeded
FATAL: Unable to copy input file "glide-grid_prot3.tmp10902.inp" to jobdb
Error: jlaunch failed.

What do I do?

Article ID: 705 - I notice that Maestro 9.1 displays F--H H-bonds. I prefer to not view these H-bonds. Can I turn them off?

Article ID: 659 - I have some problems docking a molecule that contains this fragment

C-N-(triple bonds)-C-H

After LigPrep optimization the angle of this fragment is 180. However, after Glide docking the output ligand has an angle of around 110 instead of being collinear.

Is there a solution for this?

Article ID: 575 - I tried to generate a grid for docking with Glide using the SiteMap output. I got the following warnings. What do they mean?

The input protein structure does not appear to have been prepared with the Protein Preparation Wizard.

WARNING: rdmmct(): Invalid atomic number -2, at atom of mmct 8. Atomtyping, docking will be skipped, other tasks may fail.

Article ID: 551 - How do I label individual residues of a protein? Is there a way to add text in a free format to the atoms displayed in the Workspace?

Article ID: 439 - It seems that Maestro does not update the directory when I open a new file. Often new files do not appear in the file dialog box. Is there a way to force Maestro to refresh a directory listing?

Article ID: 387 - I'd like to color hydrogens attached to nitrogens by the color of the nitrogen, and similarly hydrogens attached to oxygen should be the oxygen color (eg. red). Is this possible?

Article ID: 376 - I have a problem with the library libXaw.so.7, I cannot find it on Red Hat Linux 5. What do I do?

/opt/SCHRODINGER/maestro-v85207/bin/Linux-x86/maestro: error while loading shared libraries:
libXaw.so.7: cannot open shared object file: No such file or directory
Maestro: Could not load shared library

Article ID: 273 - At the end of Prime model building, how can I display only the built model in the Workspace?

Article ID: 272 - A homology model built on a DNA-containing template has all the DNA bases disconnected. How can the model be built with connected DNA strands?

Article ID: 263 - Can Phase shape screening be run from the command line on Windows?

Article ID: 208 - Maestro is becoming slower and slower to start. What can I do?

Article ID: 131 - Is is possible to generate a structure-based pharmacophore model from the receptor binding site?

Article ID: 120 - Is it possible to use multiple templates to build a homology model?

Article ID: 1676 - Why does a Desmond metadynamics simulation slow down as the simulation progresses?

Article ID: 1675 - I started some jobs on my Windows machine, and logged out. When I logged back in again, I found that the jobs had been killed. Why does this happen?

Article ID: 1674 - Is there a way that I can view analyses of the quality of Desmond FEP calculations?

Article ID: 1673 - Peptide Alpha Helicity jobs fail on a Mac machine or a Windows machine. Why is this?

Article ID: 1672 - When I try to compile PSIPRED on my Mac OSX machine, I get the following message in the terminal window:

make: command not found

What is the problem?

Article ID: 1638 - Where can I find out what the number of iterations and convergence criterion settings are for a Prime energy minimization job and how can I change them?

Article ID: 1621 - The free Maestro Academic Campaign license wasn't included with the academic Maestro download. How do I get the license?

Article ID: 1596 - A Glide docking job generates the message "WARNING Force field spec (null) not recognized; using default". What does this mean?

Article ID: 1595 - Find Homolog and Secondary Structure Prediction in Prime do not work. I do not have a local installation of the BLAST sequence database, so I was expecting these steps to access the NCBI site remotely. How can I fix this problem?

Article ID: 1594 - When I run a SchrodingerShell on a Japanese Windows machine, the font is too small. Is there anything I can do about this?

Article ID: 1508 - How can I zoom in on a structure in the Workspace without the clipping planes being applied?

Article ID: 1501 - How do I reorder the entry groups in the Project Table?

Article ID: 1492 - What implicit solvent model does Prime MM-GBSA use?

Article ID: 1477 - How can I change the font size of structural measurements (e.g. bond lengths) in the Workspace?

Article ID: 1473 - My job has failed, and I need help figuring out what went wrong. What should I do?

Article ID: 1443 - I would like to prepare a large ligand library using LigPrep. How should I proceed ?

Article ID: 1435 - How do I test Maestro Elements from a standard Maestro installation?

Article ID: 1425 - How do I generate an attractive, publication-quality figure in Maestro of a molecular surface of a protein colored by electrostatic potential that looks something like the image below?

Article ID: 1376 - What limits are there on the size of the system I can run with Prime?

Article ID: 1366 - How do I build a multimeric homology model with Prime using a multi-chain template?

Article ID: 1347 - Is there a way to exclude sites from consideration in the search for common pharmacophores?

Article ID: 1281 - Can I run Maestro on a remote machine and display to my local machine?

Article ID: 1255 - What is included in the MacroModel distribution?

Article ID: 1014 - I cannot get a PsiPred secondary structure prediction in the Edit Alignment step even though I have installed PsiPred on my system. What is the problem?

Article ID: 899 - The keyboard shortcuts don't seem to work correctly in full-screen mode. Is there a fix for this?

Article ID: 895 - The fonts in Maestro and Canvas aren't displayed properly. What could cause this problem?

Article ID: 816 - I chose to do web-based homology searching with Prime, and can find homologs for my query, but I get an error when trying to run the alignment job. The error is:

WARNING Errors occurred while incorporating Calculate Alignment job jobname; job record for JobID will be removed, but not the job input and output files.

What is the problem?

Article ID: 717 - What would be the best way to produce a standard input file (DICE .inp file) for Glide?

Article ID: 710 - I've noticed that Glide by default uses OPLS_2001 where as LigPrep uses OPLS_2005 or MMFF. I've been using OPLS_2005 for LigPrep. Are the OPLS_2005 parameters carried over and used in Glide? Do you recommend either switching LigPrep to OPLS_2001 or Glide to OPLS_2005 for consistency?

Article ID: 539 - While using the various tools panels in Maestro (e.g. Measurements) the view of the molecule changes because the panel takes up part of the Workspace. Is there a way to turn this feature off?

Article ID: 497 - The Multiple Sequence Viewer is a great tool, but what I'm missing is reporting of % identity and % positives (as in Prime) when doing a multiple sequence alignment on imported sequences. Is there a way to see this information?

Article ID: 488 - I want to cluster conformers, but I cannot find XCluster. What can I do?

Article ID: 481 - I have to give a presentation and would like to include pharmacophore images from Phase, to view them either in a small portable viewer or actually embedded into my PowerPoint. Is there any way to do so?

Article ID: 479 - Is there a button to get to the menu that is under Edit → Fragment?

Article ID: 464 - The GlideScore is quite low in priority in the Project Table. Is there a way to change that?

Article ID: 452 - I find that I have to start Maestro with -SGL option, otherwise Maestro terminates with segmentation fault errors. I am also having some graphics problems.

Segmentation fault
Maestro: Error while running Maestro
Maestro: ** abnormal termination **

What might be the problem?

Article ID: 437 - I notice there is a "phantom residue" that appears right next to a normal, regular residue. While the normal residue can be manipulated the phantom residue cannot. Why is it appearing and what is the point of it?

Article ID: 379 - Is there a way to customize the font size of all the menus and displayed text in Maestro? The font of the project table entries and menus are too large.

Article ID: 377 - I seem to have a problem installing the correct library. What can I do?

/opt/schrodinger/maestro-v90211/bin/Linux-x86/maestro: error while loading shared libraries: libX11.so.6: wrong ELF class: ELFCLASS64

Article ID: 296 - Submitting jobs from Windows to a remote Linux machine has stopped working, and I get this error message in the startup shell:

WARNING - POTENTIAL SECURITY BREACH!
The server's host key does not match the one PuTTY has cached in the registry. This means that either the server administrator has changed the host key, or you have actually connected to another computer pretending to be the server.
The new rsa2 key fingerprint is:
ssh-rsa 2048 fingerprint
Connection abandoned

What can I do?

Article ID: 256 - Is it possible to run shape screening over multiple CPUs, generating conformers on-the-fly?

Article ID: 238 - What default force field is used for Schrodinger modules?

Article ID: 237 - My job is in the 'stranded' status. How can I recover this job?

Article ID: 234 - I can't launch remote jobs from Windows to Linux. I get an error like:

FATAL: No usable mmshare found on remote-hostname

What is wrong?

Article ID: 210 - Does Schrödinger software include scaffold clustering ?

Article ID: 159 - I have had problems with my structures failing in Prime for various reasons. Is there a way to see if my initial structure has any problems?

Article ID: 148 - My ligands have unsupported atom types, such as boron. Is there some way I can dock them?

Article ID: 146 - How do I run Schrödinger applications from the command line under Windows?

Article ID: 88 - Can I run a ligand preparation on multiple processors ?

Article ID: 77 - How do I set up remote job submission from Windows to Linux hosts?

Article ID: 32 - When performing a docking experiment, can I constrain a ligand atom to be within a specific distance range from a receptor atom?

Article ID: 4 - Is there a way to sort columns in the Maestro Project Table?

Article ID: 1608 - How do I find the version of Prime that was current on a particular date and what is the preferred citation for that version?

Article ID: 16 - What is the Aux column in the Project Table, and what do the buttons do?

Article ID: 1632 - I have installed Maestro from the download site. Do I need a license, and how do I get it?

Article ID: 733 - What procedure do I follow if I want to mutate amino acid residues?

Article ID: 572 - How do I find the binding affinity from the GlideScore?

Article ID: 1087 - Can I change the default workspace for KNIME?

Article ID: 1671 - How do I get the error messages from Maestro on my Mac to send to technical support?

Article ID: 1670 - My Glide grid generation job doesn't even start. Is there something I can do to fix it?

Article ID: 1669 - When I start the Job Control interface from the Start menu on Windows, I get a blank page. What can I do to fix it?

Article ID: 1668 - I'm having trouble with Maestro freezing when doing some operations, and with entries that don't get included in the Workspace. I'm storing my data on an AFS file system. What's the problem?

Article ID: 954 - Can I run Schrödinger software on a Mac?

Article ID: 372 - Can I run Maestro on Linux and display to a Macintosh?

Article ID: 1667 - When building a knowledge-based homology model with Prime, the resulting model's chain ID assignment and residue numbers are not always correct. Why is this?

Article ID: 1666 - In the Maestro 9.3 MacroModel Constraints tab, I noticed that there is a 5000 atom limit on the number of allowed constraints. Is it possible to increase this limit?

Article ID: 1665 - When I installed Suite 2012 on my Windows machine, there was no information in the Software Activation screen of the installer. How do I get this information and send it in to obtain my license?

Article ID: 1664 - I want to import files into Maestro from a USB drive on my Mac, but the drive doesn't show up in the file selector. What do I do?

Article ID: 1660 - When I open the Manuals Index on my Mac, the links to the documents don't work. What is the problem?

Article ID: 1663 - I'm not getting the same results with Phase in Suite 2012 as in Suite 2011. Why is this?

Article ID: 1662 - The installation of Schrödinger Suite 2012 software onto a Mac was unsuccessful. What should I do?

Article ID: 1661 - When I run Check for Updates from Maestro in Suite 2011 Update 1, Firefox crashes when I log in. Is there a fix for this problem?

Article ID: 1658 - I double-clicked on the lic_start.bat file to start the license server, but Maestro still complains that it cannot find a license. How can I fix this?

Article ID: 1657 - How can I update the KNIME version bundled with the Schrödinger installation to use the latest release?

Article ID: 1656 - When I run a Desmond simulation, it can take a long time to copy the trajectory back to the working directory, and sometimes it fails. Why is this?

Article ID: 1655 - When I tried to run a Desmond job with Suite 2010 using a CMS file from Suite 2011, the job failed. Why is this, and can I fix it?

Article ID: 1601 - I am running a KNIME workflow from the command line. I would like to specify a different input structure file for the Molecule Reader node. How can I do this?

Article ID: 1560 - I can't start KNIME. What should I do?

Article ID: 1555 - I am using the REOS Filter KNIME node. Where can I find the definitions used, and can I modify the filtering criteria?

Article ID: 1223 - How do I find an example of the use of a particular KNIME node?

Article ID: 1148 - How can I have the license server daemon (lmgrd) start automatically when the machine is rebooted?

Article ID: 1089 - Should I be concerned if I see the message "no canvas2dGen in java.library.path" when KNIME starts on Windows?

Article ID: 1081 - Which version of KNIME is bundled with the Schrödinger KNIME Extensions?

Article ID: 1038 - Why does Glide produce duplicate poses even when a large RMS cutoff to discard duplicates is specified in the Output tab?

Article ID: 948 - How do I obtain the supporting documentation for my Schrödinger software product, and in what formats are the documents available?

Article ID: 941 - KNIME doesn't start, and produces error messages:

WARN HelpView No html browser for node description available.
ERROR Activator Error: Dynamic Library not loaded/found, cannot use Schrödinger 2D Renderer message='no canvas2dGen in java.library.path'
WARN Activator Canvas 2D Maestro Renderer is not loaded
WARN Activator Canvas 2D Sd Renderer is not loaded
WARN Activator Canvas 2D Smiles Renderer is not loaded

What is the problem?

Article ID: 814 - When I try to start KNIME with the Schrodinger extensions, I get the following error message:

WARN SchrodingerUIPlugin Cannot checkout License: basic message='Error List Returned (-513,3038) ' message='Error List Returned (-513,3038) ; Unknown Host (-14,3033) '

What can I do about this?

Article ID: 615 - Does KNIME have projects, like Maestro and Canvas ?

Article ID: 594 - Using Glide XP, I generated 100 output poses for a ligand, but I found that there were many duplicate poses, violating the default RMS deviation and maximum atomic displacement settings. What could have caused this?

Article ID: 529 - When I try to change a protein to ribbon format, the protein disappears and only small molecules are left. When I go to the terminal window, I find lots of errors there. How do I prevent this? I am displaying Maestro remotely on Windows XP using NXClient.

Article ID: 484 - How do I start a license server on a Windows machine?

Article ID: 339 - Can I close KNIME and have my workflow continue to execute, with the computations running?

Article ID: 246 - What can I do about frequent Maestro freezes?

Article ID: 177 - How can I concatenate columns in KNIME?

Article ID: 176 - Which node can I use to read in and write a text file in KNIME?

Article ID: 175 - How can inspect the content of a long text cell, such as a log file, in KNIME?

Article ID: 174 - How can I remove duplicates in a structure column in KNIME?

Article ID: 173 - In KNIME, how can I compare structure columns from two tables in order to find those that are in common, for instance?

Article ID: 171 - How can I inspect an output table from KNIME directly in Excel or OpenOffice?

Article ID: 169 - How can I see what's happening when I run a Schrödinger node in KNIME?

Article ID: 168 - How can I concatenate, fuse, or join two tables in KNIME?

Article ID: 143 - How can I copy and paste some nodes to a specific place on the screen in KNIME?

Article ID: 142 - How can I change the preferred renderer for chemical structure column types in KNIME?

Article ID: 137 - How can I easily find a KNIME node that I know the name of?

Article ID: 108 - What does this error mean?

FATAL: could not launch or verify jserver

Article ID: 24 - In my Glide docking results I am seeing multiple very similar poses for a given ligand. I thought Glide was supposed to eliminate poses with RMSD less than 0.5 Å or maximum atom displacement less than 1.3 Å, but the poses I am looking at are clearly closer than those cutoff criteria. What is happening here?

Article ID: 1654 - Can I compare two sets of compounds to get information on their similarity with Schrödinger software?

Article ID: 1028 - What tools can I use for postprocessing of the Glide docking results?

Article ID: 324 - My Schrodinger nodes do not work inside KNIME. If I execute a Schrodinger Knime node, like the Molecule Reader, in the terminal I see an error message:

WARN SchrodingerUIPlugin Cannot checkout License: basic message='No Such Feature Exists (-5,3027)
ERROR SchrodingerUIPlugin no license file found

Article ID: 1653 - What libraries do I need to install when my jobs die with the following error?

libgthread-2.0.so.0: cannot open shared object file: No such file or directory

Article ID: 1652 - When state penalties are being applied, why isn’t the “docking score” always the sum of the Epik “State penalty” and the GlideScore (“glide gscore”)?

Article ID: 1651 - What are the units for energies calculations in the Schrödinger Suite?

Article ID: 1210 - How do I get more output from a Jaguar ESP calculation?

Article ID: 1649 - My FLEXlm hostID is blank or contains all zeros (000000000000), what should I do?

Article ID: 1647 - Can I relate MM-GBSA energies to binding affinity?

Article ID: 1635 - How is the "Prime MMGBSA DG bind" property calculated?

Article ID: 1568 - How do I run Prime MM-GBSA on a complex in a Maestro file from the command line?

Article ID: 1561 - How is the Prime MMGBSA Ligand Strain Energy defined and calculated?

Article ID: 182 - My Prime MM-GBSA fails when the ligand is a peptide. What is going on?

Article ID: 1646 - What are the ranges for fitness, vector, volume, and site scores in Phase?

Article ID: 1645 - Is it possible to set up the Blast query to use a locally installed Blast database instead of using a web query?

Article ID: 1259 - Is it possible to calculate interaction energies with MacroModel?

Article ID: 1009 - How do I continue a Desmond simulation?

Article ID: 126 - If I restart a Desmond job from a checkpoint file (.cpt) from the same directory, will it overwrite the current trajectory?

Article ID: 1644 - PowerPoint crashed when I was adding the Maestro ActiveX control, after I entered and exited slide show mode. Why does this happen.

Article ID: 1455 - I can't print a PowerPoint presentation with the Maestro Viewer. Can this be fixed?

Article ID: 1454 - Can I use the Maestro Viewer ActiveX control with PowerPoint 2010?

Article ID: 837 - When I print a PowerPoint presentation that has the Maestro Viewer ActiveX control in it, I get a large X instead of the Maestro viewer. Is there a way to make it print?

Article ID: 813 - When I use the Maestro ActiveX control in a PowerPoint presentation, the graphics are scrambled. I'm running a virtual Windows machine on a Mac using VMware Fusion. Is there a fix for this problem?

Article ID: 507 - I want to use Maestro with Acrobat3D, a tool that captures the OpenGL string and transforms it into a pdf to be used in PowerPoint presentations. Though Acrobat3D recognises Maestro as a 3D application, capturing doesn't work. I assume its a problem with the x-server, as capturing from Maestro installed in an original cygwin environment doesn't work either. Would that be correct?

Article ID: 1643 - Glide docking produces poses with only chair conformations of cyclohexane rings. How can I get poses with cyclohexyl boat conformations?

Article ID: 1642 - Why should I care about the number of canonical orbitals in my Jaguar calculations?

Article ID: 1641 - Why do I get the error "cannot import name analyze" when running the Ligand Interaction Diagram?

Article ID: 1640 - I am unable to start jobs from Maestro or from the command line. I see errors like the following:

40 no reply from jserver at 127.0.0.1:41604
42 Couldn't read jserver port. Retrying....
42 $HOME/.schrodinger/.jobdb2/jserver.host.pid: pid = 19432, port = 41604, timestamp = 1316635311, refresh = 600

What is causing this problem?

Article ID: 1639 - When I click a link in one of the manuals, nothing happens. What is the problem?

Article ID: 885 - When I start Maestro, I get a message stating that a valid Maestro license key could not obtained.

FATAL -10: Unable to obtain valid Maestro license key. MAESTRO_MAIN

FATAL got_license: could not check out a license for mmlibs version version
FATAL mmerr_initialize: got_license() failed

What might the problem be?

Article ID: 564 - Is there a way to increase the maximum rotatable bonds allowed in Glide to higher than 50?

Article ID: 268 - I was trying to launch Maestro on a remote machine and display it locally via ssh with X forwarding, when this error came up. What do I do?

Maestro: Error initializing Maestro
Error: Can't open display: localmachine:0.0

Article ID: 1535 - My Phase Find Matches job stops with the following error:

PhpLigandFactory::generateLigands: The number of base features in mol_mumber does not match the number of sites stored in the database for this molecule.

How can I avoid this failure?

Article ID: 1637 - How do I change the representation of a structure in PyMOL that was transferred or imported from Maestro? The normal commands don't seem to work.

Article ID: 1558 - When I measure some distances on a frame of a Desmond trajectory, the distance marker (purple line) is plotted some distance away from the picked atoms, but parallel to where it should be. What is wrong and how can I fix this?

Article ID: 1636 - How do I take a screen shot of a panel to send to technical support?

Article ID: 1589 - I submitted a Glide docking job to our cluster a couple of weeks ago and we just had a system failure that caused our NFS disks to unmount and for the queuing system on our cluster to shutdown. Is there a way to restart the jobs?

Article ID: 656 - I started a job to screen a million molecules, and it stopped before finishing. How can I recover my results and finish the docking run?

Article ID: 18 - When I perform a Jaguar calculation, I cannot find the LUMO and HOMO values. Where are they?

Article ID: 1633 - What are the units of the surface area from the Calculate Properties panel in the Project Table?

Article ID: 1489 - I have a number of Maestro (.mae) files that I would like to merge into a single file. Is there a command for doing this?

Article ID: 1168 - Can I create a pose viewer file manually, by concatenating the Maestro files?

Article ID: 486 - I was trying to add an oxygen atom to the iron (Heme) of the P450 x-ray structure (2f9q), but Maestro did not allow it due to a "valence violation". What's the right way to do so?

Article ID: 286 - How do I combine a receptor and a ligand from separate files into a file with a single entry for the complex?

Article ID: 190 - Can I combine Maestro files or other structure files from the command line?

Article ID: 1591 - Can I use a functional for a QSite calculation that is not available from the Method option menu?

Article ID: 815 - Can I visualize molecular vibrations in Maestro?

Article ID: 959 - Are there any ring conformation templates for macrocycles that I can use?

Article ID: 1631 - What is the function of the "Mark Target Entry" option under the menu "Entry" in the project table ? How could this be used in practice?

Article ID: 1630 - The solute is outside the simulation box. What is wrong with my Desmond simulation?

Article ID: 600 - I'm studying a protein containing heme. Can Glide handle the metal coordination if the ligand is not anionic?

Article ID: 1062 - How do I perform a coordinate scan in Jaguar?

Article ID: 1629 - How can I generate dipeptide or tripeptide libraries?

Article ID: 1628 - Some Maestro panels fail to open on Windows with an error that includes 'common module unable to import OpenGL.GL'. Is there a fix for this problem?

Article ID: 1626 - How can I get started with Field-Based QSAR?

Article ID: 1625 - What is Field-Based QSAR?

Article ID: 1627 - Why don't hydrogen bonds for poses selected via Pose Filter always show up in Maestro?

Article ID: 1481 - My parallel Jaguar calculation failed with an "out of memory" error. What is the problem?

Article ID: 1020 - Is there a limit to the size of the ligands I can dock with Glide?

Article ID: 668 - Can I dock peptides as ligands in Glide?

Article ID: 337 - Is there an efficient way to filter ligands from a docking run that only make specific key interactions? These key interactions are either determined by examining the results, or through knowledge of known binders.

Article ID: 122 - When I run Desmond or Jaguar jobs on a cluster with an Infiniband network, the jobs fail with the following in the log file:

libibverbs: Warning: RLIMIT_MEMLOCK is 32768 bytes. This will severely limit memory registrations.

How can I get around this?

Article ID: 1511 - For some reason, I can't open the online help from Maestro. Is there some other way I can get access to it?

Article ID: 1624 - When I specify an external .basis and .atomig file with a path, Jaguar produces the error

FATAL: One or more input files are missing or unreadable:

This used to work in Suite 2010. What's the problem?

Article ID: 1289 - What is Atom Specification Language (ASL) and why should I use it?

Article ID: 1031 - How do I add fragments to the Build panel fragment library?

Article ID: 413 - I can't launch PyMOL from Maestro. PyMOL is installed and runs fine on our system, its path is defined and there's an alias called pymol. What seems to be the issue?

Article ID: 1556 - In the Ligand Interaction Diagram, what are the maximum lengths of hydrogen bonds, pi-pi stacking interactions, pi-cation interactions and metal coordination interactions that are identified and displayed?

Article ID: 1098 - How often are the Prime Blast and PDB third-party databases updated on the Schrödinger Prime server?

Article ID: 227 - How do I recover a project that has become corrupt?

Article ID: 1623 - On Windows, when I try to launch a job from Maestro, I get this error:

The system cannot find the path specified
61 ERROR could not launch or verify jserver
FATAL: Could not procure jserver

What do I do?

Article ID: 1622 - How is Ligand Efficiency calculated?

Article ID: 1620 - Starting with a set of query molecules, I would like to find nearest-neighbor, similar compounds based on 2D fingerprints, from a larger database of compounds. How should I approach this task?

Article ID: 1614 - How do I find the most reactive sites for electrophilic or nucleophilic attack on my substrate, and what are the electrophilic and nucleophilic atoms on the attacking species?

Article ID: 940 - Can I compute docking enrichment metrics with Schrödinger software?

Article ID: 1619 - How do I calculate the solvation energy of a molecule with Jaguar?

Article ID: 1618 - How do I calculate the binding energy of a bimolecular complex with Jaguar?

Article ID: 1617 - How do I calculate and visualize the IR spectrum of a molecule?

Article ID: 1616 - How do I calculate and visualize the UV/Vis spectrum of a molecule?

Article ID: 1615 - How do I calculate the reaction energy and activation barrier for my reaction?

Article ID: 1613 - How do I set up a transition state search?

Article ID: 1612 - What do I do if the basis set I chose does not exist for some atoms in my system?

Article ID: 1611 - Which density functional should I use for my Jaguar calculation?

Article ID: 1057 - What do I do if my Jaguar optimization stops with the message: "stopping now - optimization seems to be stuck"?

Article ID: 945 - How do I predict a molecule's ionization potential (IP) and electron affinity (EA)?

Article ID: 416 - How should I prepare reactant and product structures for a transition state search?

Article ID: 1609 - How do I prepare the ligand in my PDB structure?

Article ID: 1091 - What structure file formats can be used with the LigPrep package?

Article ID: 1607 - What is the Pose Explorer script and how is it useful in identifying promising lead compounds?

Article ID: 769 - I plan to save the best poses from SP docking into an external file and dock them using XP. Is this a good approach or is there an alternative?

Article ID: 650 - My ligand and receptor protein are in different entries. How can I combine them into a single entry?

Article ID: 456 - Our license server is stuck with this error:

lmgrd is not running: Cannot connect to license server system. (-15,570:115 "Operation now in progress")

Why would this appear?

Article ID: 824 - Why do I need to dock my library created with the Combinatorial Screening workflow in the final step again, although there was already a docking step during the library creation?

Article ID: 1605 - Every time I export (save) files in SDF format from the Project Table in Maestro, I have to uncheck the v3000 format box. Is there a way to change this default behavior?

Article ID: 1604 - My jobs fail with error messages that include 'Could not create or write to local file' and 'Could not write to remote directory'. Why is this?

Article ID: 1603 - Getting a PDB file from the web fails with the error

'module' object has no attribute 'HTTPSHandler'.

Is there a fix for this problem?

Article ID: 1602 - I set SCHRODINGER_JOBDB2 in my shell and launched some jobs. Now, I can't see these jobs, either from Maestro or using the jobcontrol utility.

Article ID: 609 - How do I cite the individual modules of your software like MacroModel, Liaison, Glide, Jaguar, etc?

Article ID: 116 - How do I cite the Schrödinger program I used in a publication?

Article ID: 338 - If I've experienced a Maestro crash, and can no longer work with my project, is there a way to recover it?

Article ID: 1599 - Can I run a replica exchange job with $SCHRODINGER/desmond?

Article ID: 1027 - What is the difference between GlideScore and Emodel, and which should I use for ranking poses?

Article ID: 1597 - Why aren't the amine groups in aryl amines (e.g., aniline) coplanar with the aromatic ring, in my Glide poses?

Article ID: 1593 - I see that my job "fizzled". What does that mean?

Article ID: 1506 - Converting a project that contains protein structures to Maestro 9.2 format failed. How can I get it to work?

Article ID: 69 - Using QSite, when can frozen orbital methods (Entire Residue and Side Chain cuts) be used ?

Article ID: 68 - I am calculating an IR spectrum with Jaguar. If some modes are Raman active, will these modes be shown in the calculated IR spectrum ?

Article ID: 67 - When performing a Jaguar calculation with solvation, the output lists Solution Phase Energy and Solvation Energy. Do I need to add these to get the total energy?

Article ID: 66 - When performing a transition state calculation in Jaguar I get the following error.

WARNING: atoms 28 and 29 are < 0.300 angstroms apart
WARNING: atoms 34 and 35 are < 0.300 angstroms apart

If I check the inter-atomic distances they seem to be fine, where is this error coming from?

Article ID: 65 - When using distance-based harmonic constraints in Jaguar or Impact, what are the units of the force constant?

Article ID: 63 - What is the scoring cutoff for "good-scoring states" in VSW? What do the "All states", "All good scoring states", and "Only best scoring state" options mean?

Article ID: 1592 - How do I get individual values for the free and the bound Liaison simulations, not just "Averaged Energy Components" values for each ligand from the log file?

Article ID: 242 - I want to generate orbitals from NBO, but when I add the PLOT keyword to the NBO section to plot the orbitals, I cannot find the orbital output files. Where are they?

Article ID: 110 - How do I change the appearance of all structures I view in the Workspace without having to change the settings each time I include something new in the Workspace?

Article ID: 1054 - How can I restart a Glide docking calculation for which some subjobs failed?

Article ID: 1493 - How can I run MacroModel jobs serially, one after another? I only have one MacroModel license, so I can't run them at the same time.

Article ID: 1564 - When docking a native ligand with Glide, how do I calculate the RMSD between the docked ligand and the ligand in the crystal structure?

Article ID: 1574 - I would like to customize the lambda schedule for FEP jobs. How can I do that?

Article ID: 1573 - My IFD job dies in the Prime stage with the error

"ERROR: Unable to read options from top-level input file"

What's wrong?

Article ID: 749 - In docking with Glide, can I get the interaction between an electrophile and nucleophile?

Article ID: 1572 - I have a small scaffold and would like to find compounds that contain the same or similar shape. Is there a way to do this using Schrödinger software?

Article ID: 1571 - I would like to run a series of IFD jobs sequentially. Is there a way to do this, so that each IFD job starts after the previous one has finished?

Article ID: 1570 - How do I make spheres and tubes smoother when using OpenGL 2.1 in Maestro?

Article ID: 1476 - I am trying to run 64-bit Maestro on a Windows virtual machine on a Mac, using Parallels, but it fails with the message "WARNING Error initializing glew". Can this be fixed?

Article ID: 1332 - Can I run Maestro on a virtual machine?

Article ID: 531 - I am running a Windows XP virtual machine on a Mac, using Parallels. I get this error when staring Maestro:

WARNING This display cannot support the graphics settings needed by
WARNING Maestro. Please try a different graphics card or see if
WARNING your graphics card can be reconfigured
Maestro: Error initializing Maestro
Maestro: ** abnormal termination **

Article ID: 1458 - What can I do to get better docking results from a homology model?

Article ID: 664 - How can I find the active site of a protein?

Article ID: 530 - My CSearch job appears to finish and I get a message saying it has been incorporated into the Project Table. However, the results aren't there, and I get this warning:

QInotifyFileSystemWatcherEngine::addPaths: inotify_add_watch failed: No such file or directory
QFileSystemWatcher: failed to add paths:

WARNING : MMPROJ ERROR(-4): mproj_incorporate_jobfe2()(): Failed to open structure file '/home/user/project/xxxx/maestro/TEST-out.maegz' for reading.
The job may have failed.

Article ID: 422 - How do I draw a simple "structureless" sequence ?

Article ID: 1569 - Running fukui.py from the command line fails with the error:

ERROR: Please specify a single input structure file
(it is allowed to contain multiple structures)

What is the problem?

Article ID: 1567 - How do I set Maestro's default working directory on Windows?

Article ID: 431 - How can I set the path in Windows for the output of Glide jobs? I notice that there is no option to browse and select a folder. Everything seems to be dumped in the same directory.

Article ID: 1412 - I am having difficulty converging a QSite calculation. Is there anything I can try that might improve the convergence?

Article ID: 51 - When I try and run a Jaguar calculation on multiple processors I get errors like this one:

ERROR: fatal error

All-analytic calculations cannot be run in parallel. Please run again with a single processor.

Why is this?

Article ID: 1566 - Maestro crashes when I open the Import or the Export dialog box. What's the problem?

Article ID: 1565 - Can I use Jaguar to calculate partial charges?

Article ID: 637 - I am trying to calculate the RMSD between the docked pose of a ligand, and the same co-crystallized ligand. Unfortunately the atom numbers don't match, resulting in an error. Do I have to renumber the atom numbers or is there any other way of doing it?

Article ID: 1563 - Installation on Windows failed with "Internal Error 2738". What do I do?

Article ID: 1562 - Installation on Windows fails with a message that includes "Base software MMShare is not applicable for install". What do I do?

Article ID: 1559 - Adding the KNIME extensions to an existing KNIME installation failed when I clicked Install. What do I do?

Article ID: 735 - I have many cases where HTVS docking skips ligands with this error message:

SKIP LIG 6150 (A-882308.0): GRID-ENERGY MIN FAILED.

However, if I do the same Glide run using SP mode then this ligand gets docked with no error message. Why does this happen? Is there some parameter I can change to eliminate or reduce this problem?

Article ID: 1557 - Maestro fails to start with an error that includes "undefined symbol: FT_Load_Sfnt_Table". What is the problem?

Article ID: 1496 - I received the following error from Maestro:

WARNING MM_MCMMonitor::reassignAllJobs(): unable to change project name for job_id JobId
WARNING [ MMjobfe library failure ]

What does this mean?

Article ID: 909 - How can I embed a G-protein coupled receptor (GPCR) in a membrane for a Desmond MD simulation?

Article ID: 903 - I get the following message when I try to start Maestro:

WARNING MM_UIMOptionMenu::setCommandID(): unknown pushbutton name: ''

What does it mean?

Article ID: 154 - I tried to align my GPCR sequence to my template using the "Align GPCR" mode and I get a Blast error "non-zero return code." What is causing this?

Article ID: 153 - I tried to align my GPCR sequence in Prime but the "align GPCR" mode reports that less than seven helices are found. What do I do?

Article ID: 152 - I have selected my GPCR template but when I run the 'align GPCR mode' my job fails to incorporate. What's wrong?

Article ID: 113 - Maestro crashed, but so far I did not save my project. Is there any place where I might find the files of the scratch project?

Article ID: 1554 - I read in a query sequence from the Workspace, and there are residues missing from the query in the Prime sequence viewer. Why is the full sequence not displayed?

Article ID: 1504 - I would like to render water sites generated by WaterMap using CPK or ball-and-stick rather than using the WaterMap analysis interface and I would then like to color the sites by free energy using the same color scheme used by the WaterMap analysis interface. I would like to do this so that I can show my colleagues WaterMap results using Maestro Scenes. Is this possible?

Article ID: 344 - When I have a protein-ligand complex in the workspace is there an easy way to unclutter the Workspace? I only want to see relevant information such as the ligand, a small surrounding part of the protein and distinctive rendering.

Article ID: 59 - I tried to use Prime with the thirdparty databases mounted on an NFS directory, but I received the following message:

nss-shared-helper: Shared database disabled (set NSS_USE_SHARED_DB to enable)

Where do I have to set this environment variable?

Article ID: 58 - I tried the hydrophobic/hydrophilic surface view, but I noticed that changing the isovalue changes the view dramatically. What exactly is this?

Article ID: 52 - When I try and open a panel from Maestro or run some Python script, it fails and I get errors like this:

WARNING Error in executing: ' qpld_gui.panel' :
Error type: exceptions.NameError
Error message: name 'panel' is not defined

Why is this?

Article ID: 47 - Is there any way of performing a fast semi-empirical calculation with the Schrödinger suite?

Article ID: 408 - Is it possible to define the chirality in a structure while building it?

Article ID: 407 - How do I flip the chiral center for a bicyclic system?

Article ID: 392 - To change the chirality of a particular carbon atom, say, in a steroid skeleton, I would have to break a bond next to it, adjust the dihedral angle of the other attaching atom and re-connect to the opposite chirality mode. Is there an easier way to accomplish this?

Article ID: 872 - I tried to start Maestro on a remote machine, displaying to my workstation, but it does not seem to be displaying correctly. What can I do to fix this?

Article ID: 573 - Can I calculate binding affinities with Schrödinger software?

Article ID: 518 - Maestro fails to start and produces error messages. What can I do?

Article ID: 446 - Maestro crashed immediately upon start up. The beginning of the message in the Maestro_error.txt file is:

DISPLAY
GRAPHICS Unable to determine graphics

What is the problem?

Article ID: 1537 - How do I run ICDA to produce an all-atom structure of a protein?

I read about ICDA (Independent Cluster Decomposition Algorithm) in these two papers: The VSGB 2.0 model: A next generation energy model for high resolution protein structure modeling, Jianing Li, Robert Abel, Kai Zhu, Yixiang Cao, Suwen Zhao, Richard A. Friesner, Proteins: Structure, Function, and Bioinformatics. and Assignment of polar states for protein amino acid residues using an interaction cluster decomposition algorithm and its application to high resolution protein structure modeling Xin Li, Matthew P. Jacobson, Kai Zhu, Suwen Zhao, Richard A. Friesner Proteins: Structure, Function, and Bioinformatics, 2007, 66 (4), 824-837

Article ID: 1536 - Is there a way to tell if a ring is aromatic or not, using Jaguar?

Article ID: 1528 - When installing the software, installing the license, running the "machid" program, or running Maestro, I get the following unusual message:

556: Illegal number: unknownunknown

What should I do?

Article ID: 1534 - When I select a Phase database in the file selector for a Find Matches job, the name doesn't appear in the "File name" text box. What's wrong?

Article ID: 31 - How should I treat water molecules in the active site while preparing my target structure, and how does Glide treat water molecules that are in the active site?

Article ID: 1533 - I see errors like the following in the log file from a parallel job:

mca: base: component_find: unable to open
$SCHRODINGER/mmshare-v20109/lib/Linuxx86_64/openmpi/lib/openmpi/mca_btl_openib: perhaps a missing
symbol, or compiled for a different version of Open MPI? (ignored)

What is wrong?

Article ID: 1532 - Can I superimpose conformers based on a subset of the atoms in the structure, like all heavy atoms, or the atoms in a particular ring?

Article ID: 1531 - Is it necessary to align all the non-model ligands before proceeding to the Build QSAR step in the Phase Develop Pharmacophore Model workflow?

Article ID: 1529 - Searching for homologs in the Prime Structure Prediction workflow fails with this error in the log file. What's the reason?

INFO: installation/thirdparty/database/blast does not appear to be available
ERROR: unable to run local job, aborting.
ERROR: Unable to assemble blast command

Article ID: 1371 - In the Structure Prediction workflow, there is an error message in the log file indicating that the Blast environment could not be set up. How do I fix this error?

Article ID: 1360 - I want to install Prime, and my site already has a local copy of the PDB. What should I do to use this copy?

Article ID: 1359 - I have previously installed the Blast and PDB databases and software, and they have successfully been used by Prime. Now I want to update these databases. What should I do?

Article ID: 692 - In spite of the fact that the ranking is performed by Emodel, Post Docking minimization seems to minimize the GlideScore. Could you explain the reason behind this?

Article ID: 1527 - How can I export the aligned structures in the Score Hypotheses step of the Develop Pharmacophore Model workflow?

Article ID: 1526 - Is it possible to run a Phase shape-based search over multiple processors when searching a database with conformers?

Article ID: 1090 - I have a receptor/ligand pair with an unknown experimental binding energy, and I want to use Liaison to determine the computed binding energy. How do I calculate the ligand's binding energy, and how do I ensure that the calculated value for the ligand/receptor pair is realistic?

Article ID: 770 - Is it possible to calculate the binding constant (K) using some of the energies resulting from the Glide docking process?

Article ID: 1523 - I am trying to run the Protein Preparation Wizard from the command line with -NJOBS for multicore processing but I am getting this error message:

PDB format is not supported for StructureWriter
RuntimeError: PDB format is not supported for StructureWriter

What is the problem?

Article ID: 1522 - Can I set up a hot key that will add R/S labels to all chiral atoms in a structure in the Workspace?

Article ID: 1514 - When I run Protein Structure Alignment in Maestro or structalign from the command line on pairs of proteins separately I get slightly different alignments compared to when I run on the full set of proteins all together. For example,

$SCHRODINGER/utilities/structalign <pdbid1>.pdb <pdbid2>.pdb <pdbid3>.pdb

gives a slightly different alignment than

$SCHRODINGER/utilities/structalign <pdbid1>.pdb <pdbid2>.pdb
$SCHRODINGER/utilities/structalign <pdbid1>.pdb <pdbid3>.pdb.

Is this a bug?

Article ID: 1521 - Why are the Jaguar energies for the LACVP or LACV3P basis sets so different from those with other basis sets?

Article ID: 1518 - Why don't I see any effect when I change the "Resting Resolution" slider settings in the Molecular Representation panel or in the Preferences panel under Molecular Representation → Atom and bond quality?

Article ID: 1517 - Why do I get better quality figures when I save the Workspace image with OpenGL 1.2 than with OpenGL 2.1?

Article ID: 1510 - When I change an atom type (retype) in Maestro, the length of the bond to the atom I retyped changes. How do I make it so this does not happen?

Article ID: 547 - Could you let me know where I could find the atom type parameter files for OPLS_2001 and 2005?

Article ID: 1513 - Molecules disappear off screen and their coordinates change excessively when performing local translations or rotations. What can I do to fix this behavior?

Article ID: 1498 - When I try to start the license server, I get this error message:

ERROR: Some required files are missing from :
hunt platform

What is going wrong?

Article ID: 1437 - When I run $SCHRODINGER/machid or $SCHRODINGER/licadmin, I get the following error:

/usr/bin/ldd: $SCHRODINGER/mmshare-vXXXXX/bin/Linux-x86_64/lmutil: /lib64/ld-lsb-x86-64.so.3: bad ELF interpreter: No such file or directory

What do I do?

Article ID: 1509 - How do I use the Atom Selection Dialog (ASD) in Maestro to, for example, render the molecular representation of specific helical residues on a protein as CPK?

Article ID: 1072 - How can I use my own Python libraries with the Schrödinger Python API in Python-based KNIME nodes?

Article ID: 1296 - How can I zoom in on the structure in the clipping planes window?

Article ID: 1507 - I would like to run Prime with user-defined charges on, for example, unnatural side chains and methylated protein backbone. How do I do this?

Article ID: 326 - I am trying to run a job on a remote Sun Grid Engine (SGE) cluster, but my job hangs in 'submitted' status. The user name on my local machine is not the same as on the cluster. What do I do?

Article ID: 278 - Does Schrödinger support computation on the GPU via GPGPU technology such as CUDA (NVidia), Stream (ATI), FireStream (AMD) or OpenCL?

Article ID: 1505 - What do the Quality, Balance, and Performance options on the Rendering button of the Style toolbar actually do?

Article ID: 855 - When I ran a combinatorial library enumeration with CombiGlide, there were fewer structures returned than I expected. Why is this?

Article ID: 939 - Where can I find instructions for installing PSIPRED for use with Prime?

Article ID: 936 - It is possible to calculate the IC50 value of a ligand-receptor complex with any of the Schrödinger software?

Article ID: 793 - How accurate are the XP GlideScores?

Article ID: 763 - Can the Glide settings be changed so as to obtain a correlation between the score values and their experimental Ki and IC50 values?

Article ID: 560 - I want to perform ensemble docking of 50 substrates, using the conformations (about 500) of an apo protein generated by molecular dynamics, with Desmond. How do I go about this?

Article ID: 553 - How do I use an ensemble of receptors derived from IFD for virtual ligand screening?

Article ID: 191 - Can I view the details of the PLS model I generated in Canvas?

Article ID: 144 - GlideScore/Docking Score doesn't correlate with my known activities. What is wrong?

Article ID: 28 - What is ensemble docking and how can I use it?

Article ID: 1503 - I want to create an image that shows the sequence alignment of just the binding site resiudes for several receptors. How do I do this?

Article ID: 1502 - How do I find where the included entries are in the Project Table?

Article ID: 1500 - I want to use a red-green-blue color ramp to map an electrostatic potential onto a surface, but there isn't one available. Can I create my own color ramp?

Article ID: 1499 - My Glide docking job produces the following message:

TOO MANY WATER SITES 2000001

What does this mean?

Article ID: 1497 - I'm building a homology model on a template that has a gap, but the conformation of the residues on either side of the template gap are not kept. How do I ensure that the conformation is retained?

Article ID: 1494 - Why do I get different alignments when importing a homolog into the Prime Structure Prediction panel and when selecting the same homolog in the results of a search for homologs?

Article ID: 1484 - How are Prime MM-GBSA calculations carried out, and what solvation model is used? Is this described somewhere in the literature?

Article ID: 1035 - Why do I get fewer poses per ligand than requested?

Article ID: 888 - I have two monitors attached to my Linux machine (one stereo-capable, the other not). I want to set up my system so that I can see the Workspace in stereo on one monitor, and the Project Table on the other. Is this possible?

Article ID: 861 - I want to create a Phase hypothesis by adding some sites using a ligand, then adding others by placing them in a chosen location. When I switch from the Ligands tab to the Freestyle tab, the sites I added disappear. How do I get these sites into my hypothesis?

Article ID: 842 - A Glide 5.5 XP fragment docking job dies with the log file error

%IMPACT-E: Insufficient storage for pointers. pointer set at 1501

What does this mean?

Article ID: 810 - While generating pharmacophores using 5 actives, I got the following warning message:

WARNING No hypotheses survived the scoring job. Try relaxing the scoring parameters.

Can you tell me how to change the scoring parameters, or what else I can do?

Article ID: 788 - I can run Maestro, but Glide fails with the following error:

FATAL mmim_handle_start(): error launching sh installdir/glide -OVERWRITE -PROJ ... What is the problem?

Article ID: 775 - How do I dock to a receptor like hERG without knowing if the drug is an activator or a blocker? hERG has a large inner cavity for receptor blocker ligands and pore domains and some external cavity activators.

Article ID: 732 - I'd like to retain the first 1000 poses with lowest energy for a ligand when I do docking in Glide. Although I specified "write out at most 1000 poses per ligand", the real output only gave me 2 ligand poses. How do I get more poses?

Article ID: 725 - I got the following error message from a Glide docking run with a ligand that has a large ring:

Impact: WARNING calculate_priority(): unexpected sidechain atom name: ' N1 '
Failed to generate ring conformations

What do I do?

Article ID: 709 - In my Glide input I used the keyword GRIDFILE to specify the name for my receptor grid. When I run Glide from the command line with this input file the grid is always written to grid.zip. Why is this keyword being ignored?

Article ID: 682 - I cannot define a core in a molecule of more than 25 atoms or so, for a Glide core constraint. I am getting the SMARTS pattern from the Workspace, but it seems that the SMARTS pattern is too long. How do I go about this?

Article ID: 667 - When I tried to divide a Glide job into 10 subjobs and used 10 CPUs to run it, only 7 of the 10 passed, while 3 died. Is there a maximum number that a job can be divided into?

Article ID: 642 - In my receptor there is a cofactor (Zn) that interacts with 3 different residues of the receptor and also with the ligand. Should I delete the bond between the cofactor (Zn) and the ligand before running Glide?

Article ID: 638 - I have a structure and a predicted binding site, and millions of compounds to dock, but no known actives. Is there any way to predict the things that are going to be active and exclude things that are almost certainly going to be inactive?

Article ID: 631 - I created a 6-membered ring in boat conformation and want to create the template. Running the script $SCHRODINGER/utilities/ring_templating gives the error:

Templates for all existing rings are already present.

What has gone wrong?

Article ID: 622 - Does the ConfGen Advanced feature "Use n steps per rotatable bond" refer to uniformly distributed torsion values (with a fixed torsion grid increment) or is it something else?

Article ID: 610 - I have a complex, with the ligand and protein in separate PDB files, in the same coordinate frame. I'd like to make a grid file on the command line. Is there a way I can do so and specify the grid center using the ligand?

Article ID: 603 - It seems that the merging of XPDES files from Glide subjobs fails under certain conditions. How can I generate a merged file from a set of subjob files?

WARNING: Could not find subjob XPDES file 'filename_glide-dock_XP_'subjobnumber'.xpdes

Article ID: 586 - What does the following Glide error message mean? How do I get around it?

checkcorepos(): Core centroid is beyond tolerance 1.000000 of grid box.
%IMPACT-E (die): At line 36
%IMPACT-E: Reference structure check failed; cannot use core constraints.

Article ID: 585 - I specified 3 poses per ligand for DOCK_POSES_PER_LIGAND, but my "lib" file (with all the docked ligands) only has one structure per ligand (15 in total). Is there something else I need to do to get 3 poses saved per ligand?

Article ID: 580 - When running LigPrep on a cyclic peptide with cis amide conformations, the amides stay in the cis conformation rather than changing to trans, which is the correct conformation. How do I fix this?

Article ID: 579 - I used the refine option in Glide for a series of analogues, which I expected to all produce results. However, two of the structures did not appear in the pose viewer file. What might the issue be?

Article ID: 576 - My Glide runs fail with the following error

Unable to locate file sgb.param.
Make sure IMP_ROOT or IMPACT_EXEC is set.

What might the problem be?

Article ID: 555 - When I submit Glide jobs from Maestro, they always run at very low priority. Assuming that I don't want to nice my other processes down, how do I make it so that Glide runs with with a higher nice value automatically?

Article ID: 533 - In Maestro 9.0.111, exporting entries to individual files in SD format, using entry names as the file names, does not work since it can only export in .mae format. What seems to be the problem?

Article ID: 524 - The workspace sequence viewer keeps crashing. Why does that happen?

Maestro received SEGV signal (memory access error) QWidget::repaint: Recursive repaint detected
Maestro: Error while running Maestro
Maestro: ** abnormal termination **

Article ID: 523 - After upgrading to the latest version, a while after Maestro starts the computer locks up whenever I try to do something like build or rotate a molecule. What is going on?

Article ID: 521 - I cannot write files or submit jobs from Maestro. The error displayed in a dialog box was:

WARNING mmim_handle_set_arg(): set operation failed: string not allowed for variable: qsite_ff
FATAL mmim_handle_set_arg_string(): error in setting string value.

What is the problem?

Article ID: 502 - I have 6 protein structures aligned and I want to emphasize the amino acids that are different. How can I do this without having to go through all six sequences and coloring each residue manually?

Article ID: 500 - When running setup.exe to install Maestro on Windows, I kept getting the error message

[Log 1] FATAL: Schrodinger Installer requires maestro-v or GUIDs.ini file.

and the installation fails. What is the problem?

Article ID: 494 - In panels such as Change Directory or Import Structures, Maestro does not show most of the folders or files present in a directory. I can type in the folder name, and it will change directory properly, and after doing so Maestro might show the folder. How do I fix this?

Article ID: 477 - When adding N terminal residues to a protein, the coordinates are added to the end of the coordinate list. Is there a way of putting the coordinates in residue order?

Article ID: 458 - Could this message be a problem with the license server?

FATAL mmlic3f_license_expiration: Cannot determine expiration date

Article ID: 428 - When I try to align protein structures I get an error:

Problems occurred during the protein structure alignment.
The structures were not aligned

How do I proceed?

Article ID: 410 - I'm starting from crystallographic coordinates for a ligand from a protein/ligand complex. I would like to compare the RMSD of the generated conformers to the crystallographic coordinates. How do I do that?

Article ID: 384 - When I exit Maestro 9.0, displayed on Windows, there is a program error with OpenSuSE 11.1, on the NX server. What do I do?

Maestro received SEGV signal (memory access error).
WARNING The m2io library has not been initialized.

Article ID: 374 - On trying to start Maestro I get this error. What does it mean?

schrodinger_dir: error while loading shared libraries:
/home/schrodinger/maestro-v90111/lib/Linux-x86/libifcore.so.5: cannot restore segment prot after reloc: Permission denied

Article ID: 369 - An error message is displayed while loading Python modules when Maestro starts. What do I do?

ImportError: No module named core ...
ImportError: numpy.core.multiarray failed to import

Article ID: 327 - Maestro crashes every time I try to open a pdb structure or a folder, with this error:

Fatal error: Loading module SGEDRV.dll failed (Error #126) !

I'm running on Windows. What can I do to fix this?

Article ID: 317 - In QSite versions before Suite 2009 (QSite 5.5), MM interactions from frozen atoms were not counted during optimization. Newer versions however count everything. Is there a way to control inclusion/exclusion of frozen MM interactions?

Article ID: 316 - When I tried to submit a job to a remote node, I get the following error message:

"Host key verification failed"

What can I do to fix this?

Article ID: 280 - With Maestro 9.0 I am having problems submitting jobs from a Windows client onto the cluster. The jobs appear in the queue on the cluster and the queue says they are running but all the job monitor on the Windows client prints out is dots. What is wrong?

Article ID: 269 - Is it possible to do a local workstation installation and open Maestro locally while running the longer jobs on a cluster? For this kind of installation, will the license file need to be set up locally as well?

Article ID: 265 - What force field is used for geometry-like calculations and analysis (e.g., molecular surfaces, vdW parameters) in Maestro? Can the parameters be modified?

Article ID: 222 - I installed Suite 2009 on a 64-bit Linux platform (Centos 5.4). When starting Maestro I get the error message:

/schrodinger/maestro-v90211/bin/Linux-x86/maestro: error while loading shared libraries: libGLU.so.1: cannot open shared object file: No such file or directory
Maestro: Could not load shared library

The program does not start. Is there a way around this problem?

Article ID: 163 - I have a large number of conformers, and I want to reduce the conformer population by running a multiple minimization with redundant conformer elimination. It appears that I can save no more than 10,000 resulting conformers. How can I save more than 10,000 conformers?

Article ID: 162 - When I perform a QSite calculation the output file contains the coordinates of the QM atoms, but not the MM atoms. The restart file contains the MM and QM atoms, but this is just for the final step. Can I obtain all the coordinates for the different geometries during the calculation?

Article ID: 160 - I have built my GPCR homology model and I am confident the alignment is correct. I want to rotate a helix to help orient a known key residue into the binding site. Can I do this in Maestro?

Article ID: 90 - I have two trajectories that I want to merge and view in Maestro. Is there a way to do that?

Article ID: 56 - In a Glide docking study, I requested 15 poses but I received feedback that the degeneracy check includes only 10 poses. Is Glide checking all of the poses in the output or is the number of checked poses internally limited?

Article ID: 45 - Our weekly cron script is telling us that no PDB files were synced this week. Is there something wrong with your server? The cron runs the following command:

$SCHRODINGER/utilities/rsync_pdb

Article ID: 44 - I am trying to do a MM-GBSA calculation with Prime. When the protein is entirely frozen, it works fine, but if I specify a flexible region > 0 Å, then subprocesses of the calculation die and I don't get any results. What could the problem be?

Article ID: 34 - I ran the entire core hopping procedure and I thought it would output the same results as running the core hopping alignment followed by HTVS in Glide using the dressed library. However, the results are different. Can you help me to understand why?

Article ID: 8 - When importing a .map file, I get the following error each time.

FATAL: mmvisio_read_cns(): Found invalid title (1 of 84).
WARNING: MMPROJ ERROR(-4):
mmproj_index_entry_import_cns()
Failed to read CNS file '/filename.map'

Why is this happening?

Article ID: 1495 - When I start a Desmond job on a Windows machine, the job never runs. What is the problem?

Article ID: 1490 - When I tried to import a structure into Maestro, I get this warning:

"WARNING No project is currently open."

When I tried to create a new project, I got this warning:

"WARNING Cannot create new project '/home/user/a.prj'.

And when I tried to open an existing one, I got this warning:

"WARNING Cannot open project '/home/user/myProject.prj'.

This is a new problem that I have not observed before. How do I fix this problem?

Article ID: 1487 - What are the "metal-binding states" produced by Epik, and how are they used?

Article ID: 1436 - I got the following error when trying to build a homology model in Prime:

WARNING Errors occurred while incorporating Build Structure job

In the log file, I see this error message:

ERROR: mismatch in length of COMPOSITE_ARRAY and query sequence for template template1_A

Article ID: 1110 - When I try to run Python scripts or open some panels in Maestro I get a traceback that ends with

_tkinter.TclError: unknown color name "gray90"

followed by several error messages

"WARNING MM_Monitor::initializeJobHandle(): error getting job end time for job end time"

What is the problem?

Article ID: 1108 - A particular sequence gave the following error when I tried to run SSpro locally:

ERROR: query sequence in alignment different from query sequence given on cmdline
ERROR: unable to pad alignment
ERROR: unable to convert Blast output to SSpro format
ERROR: parsing blast output

Any idea what the problem might be?

Article ID: 876 - I would like to export the results of a SiteMap analysis into another format so I can use special visualization software like PyMOL to create pictures for publication. Since the results are principally just surfaces, they don't have any coordinates. Is there another way to save the SiteMap grid points as pseudo atoms?

Article ID: 875 - When I submit jobs to a remote host from Windows, I get a missing directory error message in the Maestro startup shell:

Error: Directory C:\Schrodinger2009 missing on host

I have set up connections from Windows to the remote host and verified with the SchrodingerPlinkWizard that it works. Whats wrong?

Article ID: 849 - Maestro fails with the error message

install-dir/mmshare-vversion/bin/Linux-x86/python: can't open file
install-dir/mmshare-vversion/bin/Linux-x86/toplevel.py': [Errno 2] No such file or directory

I get the same message if I try to run jobs. What is the problem?

Article ID: 828 - I am trying to restart a QST transition state search with Jaguar, but it fails with the message:

Oops, geometry 2 contains different atoms (or atom labels) from the initial geometry. This must be resolved before running the job.

How can I fix this problem?

Article ID: 762 - When I try to run the Ligand Interaction Diagram script on Windows, I get this error:

Error in executing: 'ligand_interaction_diagram_gui.panel' :
Error type: <type 'exceptions.ImportError'>
Error message: No module named render

What is the problem?

Article ID: 745 - I get the following message when running Glide:

%IMPACT-W (warning): At line 63
%IMPACT-W: Ligand lacks atoms to satisfy receptor constraints.
SKIP LIG 23631 (ligand_23631): INVALID ATOM(S), ETC

What does it mean, and what can I do about it?

Article ID: 738 - I have two receptor structures: one is a crystal structure in the open conformation with iron and cofactor only, the other is a model in the closed conformation with both iron, solvent (which occupies the cofactor position) and substrate. The difference between the two structures is the flap region opening or closing. How should I go about finding inhibitor candidates with Glide?

Article ID: 718 - When I run para_glide it returns this error:

"Error: The input file 'glide_docking.in' does not appear to be a DICE input file."

The input file I am providing is simply the one I took from the output of a Maestro-initiated Glide-XP job. What went wrong?

Article ID: 678 - According to the manual, the names of the Glide pose file properties should have the form 't_o_d' - type,owner,data. However, in the Glide output the item names have an additional one letter field which is usually filled by letter 'i' or 'r':

i_i_glide_lignum
r_glide_XP_GScore.

Could you explain how the Glide names should be interpreted?

Article ID: 657 - I get the following error when generating a grid with flexible hydroxyls:

FATAL mmim_handle_write_rec_glidecons(): Found constraints to movable atoms, or check failed.
FATAL mmim_handle_check_cons_to_flex(): error determining specification of movable atoms.

How do I fix this?

Article ID: 569 - While attempting to dock a ligand , I keep getting these errors. Is there a solution for this?

%IMPACT-E (die): At line 10
%IMPACT-E: CREATE: Atomtyping failed with current force field.
%IMPACT-I(foldmain): parameter assignment not performed

Article ID: 527 - I made some changes to the display of InducedFit that I did not like and now I can't seem to get back to the original. Even if I exit Maestro and re-open the project, it still gives me the messed-up view. It looks like my results got all over-written, automatically. Is there any other way to fix it apart from a re-run of a long computation?

Article ID: 525 - I am trying to use Align Binding Sites to align two kinase binding sites, but I get this error message:

ERROR: Less than 3 receptor atoms found within 10.00 A of ligand atoms in first file...exiting.

What would the best options to use be in order to get it to run?

Article ID: 516 - I'd like to create a surface for the entire chain A and then limit its display by proximity to chain E but without calculating the whole surface. This doesn�

Article ID: 509 - When I clicked on the "." in the Import panel an error message appeared after which Maestro crashed. What do I do?

QTreeView::rowsInserted internal representation of the model has been corrupted, resetting.
Maestro: Error while running Maestro
Maestro: ** abnormal termination **

Article ID: 508 - I just finished optimization of a big molecule with Jaguar when I found that the surface I requested was clipped at the ends of molecule. How do I correct this?

Article ID: 493 - In the Suite 2009 Protein Reports tool, clicking the rows under "steric clashes" gives a message each time I click on a new row: "Workspace has changed, and data may no longer be valid. Please use the update button". The update button works but the process takes too long. Is there any workaround for this?

Article ID: 451 - The results of the rmsdcalc script, used to perform alignment and rmsd calculations, are not consistent with what I obtained from the Superposition tool in Maestro, and I think that the result from the Maestro tool is more reasonable. Is it possible to use the "superposition" utility from the command line?

Article ID: 450 - I get this error when I start Maestro. What does it mean?

WARNING Minimum of 16-bit depth or greater, double buffered, non-stereo visual needed. This was not available.
WARNING FATAL Problem: Could not get visual
Maestro: Error initializing Maestro

Article ID: 380 - I get this error when I start Maestro. What is the problem?

/net/software/schrodinger2009/maestro-v90109/bin/Linux-x86/maestro:relocation error:
/net/software/schrodinger2009/mmshare-v18109/lib/Linux-x86/librt.so.1:symbol __pthread_clock_settime, version GLIBC_PRIVATE not defined in file libpthread.so.0 with link time reference
Maestro: Could not load shared library

Article ID: 375 - I just installed some updates to my computer and now I find that Maestro is not working. What is the problem?

Could not create rendering context
MM_GLW.init(): could not create rendering context
Maestro: Error initializing Maestro
Minimum of 16-bit depth or greater, double buffered, non-stereo visual needed. This was not available.

Article ID: 370 - I just installed the latest version of Schrödinger software on a new computer and I am receiving some OpenGL GLX errors. What do they mean?

X server has no OpenGL GLX extension.
Try a different display or try enabling GLX in your X Server or invoking Maestro with -SGL. (Using -SGL results in 3D graphics being done in software and may significantly reduce graphics performance.)

Article ID: 360 - Optimizing the H-bond assignment results in an error like:

File "schrodinger\protein\assignment.py", line 449, in enumerate_states
if ct.measure( iatom, iacceptor ) < 2.0:
File"schrodinger\structure.py", line 3162, in measure self.handle, atom2)
TypeError: an integer is required

What is going wrong?

Article ID: 329 - I have some PDB files that I want to convert into Maestro format and put in one file. I converted the first file into Maestro format with the structconvert command, then used option -a to append the second file into the first Maestro file. However, it didn't work as I'd expected. The error message is "Unknown option -a". How do I use this utility?

Article ID: 297 - I accidentally deleted my publickey.txt file on Windows. Now I cannot configure access to a new remote host. Do I have to regenerate all my ssh keys?

Article ID: 293 - When trying to generate a Glide grid for a receptor with flexible hydroxyls, why do I get the following errors in the terminal when the job is launched?

FATAL mmim_handle_write_glide_setup_recep_task(): error reading flexible receptor groups ASL.
FATAL mmim_handle_write_glide_job(): error in mmim_write_glide_setup_recep_task.
FATAL mmim_handle_write(): unable to write tasks to input file.

Article ID: 292 - When I run the Fingerprint Generation node in KNIME I got this error message in the KNIME Console:


ERROR	 Fingerprint Generation	 Execute failed: SCHRODINGER variable not set

I am using the latest KNIME on Windows from knime.org and have installed the Schrödinger KNIME Extensions from KNIME using Help → Software Updates. What should I do?

Article ID: 289 - When docking a large database, why does Glide sometimes fail with an error like the following?

posesort(): error 256 executing glide_sort command; will try 1 more time
Out of memory!

Is there a workaround, or a way to recover the intermediate results?

Article ID: 260 - I have previously written GAMESS format files (*.gamin) directly from Maestro for small molecules with previous versions of Maestro. I notice that the *.gamin files produced appear to no longer be in the same file format and have no header information as they did before. Has something changed and is there a way to write out a GAMESS input file from Maestro?

Article ID: 236 - Jaguar jobs submitted to a queuing system produce errors like the following:

jaguar: WARNING fifo_write(): open(): No such file or directory
jaguar: WARNING fifo_write(): Unable to open /tmp/5868.1.all.q/jmonitor14955
Error: Unable to open job control link for writing

What is wrong?

Article ID: 225 - What does this error I get on starting Maestro indicate?

WARNING This display cannot support the graphics settings needed by
WARNING Maestro. Please try a different graphics card or see if
WARNING your graphics card can be reconfigured
Maestro: Error initializing Maestro
Maestro: ** abnormal termination **

Article ID: 223 - I get this warning message when Maestro starts. What do I do about it?

X Error: BadAlloc (insufficient resources for operation) 11
Extension: 147 (Uknown extension)
Minor opcode: 3 (Unknown request)
Resource id: 0xa00473
X Error: GLXBadContext 148
Extension: 147 (Uknown extension)
Minor opcode: 6 (Unknown request)
Resource id: 0xa00475
X Error: GLXBadContext 148
Extension: 147 (Uknown extension)
Minor opcode: 5 (Unknown request)
Resource id: 0xa00475
QGLContext::makeCurrent(): Failed.

Article ID: 221 - I get the following error message on starting Maestro. What does it indicate?

/home/user/myinstall/maestro- v90111/bin/Linux-x86/maestro:
/lib/tls/libpthread.so.0: version `GLIBC_2.3.3' not found (required by /home/user/myinstall/mmshare-v18111/lib/Linux-x86/librt.so.1)
Maestro: Error initializing Maestro

Article ID: 150 - When I start Maestro, I am getting error messages like:

WARNING : MMDBI ERROR(-4): mmproj_dbi_db_open(): Failed to set the pragma
WARNING : MMPROJ ERROR(-4): mmproj_project_new(): failed to open the entryproperties database.
failed to create scratch project in '/scratch/user'
WARNING MM_DGOList::draw(void): Could not draw DGOList SurfaceMC, DGO SurfaceDGO
WARNING MM_DGOList::draw(void): Could not draw DGOList SurfaceMC, DGO SurfaceDGO

What is the problem?

Article ID: 79 - I am trying to set up a simulation of a P450 enzyme which has a heme group with an iron atom (+3 charge) covalently bonded to four nitrogen atoms in the heme group, and to a sulfur atom in a cysteine. No matter what I've tried I always get a "valence violation" when I try to connect the iron atom to the cysteine sulfur using Maestro. How can I do this?

Article ID: 57 - Which scoring terms are included only in GlideScore XP, which ones are common to SP with identical weights, and which ones are used in both scoring functions with different weights?

Article ID: 43 - When I try to start Maestro on Linux Fedora 12, I get the following error in the terminal:

Minimum of 16-bit depth or greater, double buffered, non-stereo visual needed. This was not available.
WARNING Minimum of 16-bit depth or greater, double buffered, non-stereo visual needed. This was not available.
WARNING FATAL Problem: Could not get visual
/home/schrodinger/maestro-v85207/bin/Linux-x86/startup:
line 984: 11474 Segmentation fault $MAESTRO_EXEC/splash
Maestro: Error initializing Maestro
Maestro: ** abnormal termination **
Generating report information...

---

What can I do?

Article ID: 13 - My Desmond simulation crashed with the following error message. How do I avoid this?

INCREMENT_POSITION((p[n])->y=0.421262,( _vm3*_vx + _vm4*_vy + _vm5*_vz )=-3.71935) produced an out-of-range result; the simulation likely is either unstable, producing NaNs or has too large an interval between migrations

Article ID: 9 - When running parallel Jaguar or QSite calculations the following message is in the log file for the job. Is this a problem?

[[6789,1],1]: A high-performance Open MPI point-to-point messaging module was unable to find any relevant network interfaces:
Module: OpenFabrics (openib)
Host: hlwus019
Another transport will be used instead, although this may result in lower performance.

Article ID: 5 - If, after a Jaguar QM calculation, I realign the molecule using the Maestro superimpose tools to bring the orientation of the molecule in line with a reference compound, the dipole moment doesn't move with the molecule and so the dipole moment is no longer correct for the displayed structure. Is there a workaround for this (other than aligning molecules before doing the QM calculation)?

Article ID: 1470 - Sometimes the results returned from Glide have slightly distorted aromatic rings. Can I prevent this?

Article ID: 1439 - Can molecular descriptors be calculated with Schrödinger software, including topological and connectivity descriptors?

Article ID: 1431 - How do I build a multi-chain homology model (multimer) with Prime v3.0 / Maestro v9.2 (Suite 2011)?

Article ID: 1430 - What does the abbreviation "PBF" stand for in the jaguar software solvation model?

Article ID: 1386 - Which physical properties does QikProp predict?

Article ID: 1382 - What is QikProp and how can it help my research?

Article ID: 1352 - What is Induced Fit Docking and how can it help my research?

Article ID: 1340 - Can I generate a hypothesis in Phase from a prealigned set of ligands?

Article ID: 1339 - Why do sulfone oxygens have 3 lone pairs by default?

Article ID: 1319 - How can I apply a task to a selection of atoms in the Workspace?

Article ID: 1317 - Workspace operations don't work when I display to a second monitor on Windows. What can I do?

Article ID: 1312 - Maestro crashes when I try to print a structure. What can I do?

Article ID: 1311 - How do I use the hardware-accelerated OpenGL graphics capability of my NVIDIA video card under Linux?

Article ID: 1310 - Maestro fails on startup with an error message that includes "cannot restore segment prot after reloc: Permission denied". What can I do?

Article ID: 1309 - Maestro fails to start on OpenSuse 10.3 and Fedora 8. What can I do?

Article ID: 1305 - Why is the progress of my job not updated in the Monitor panel?

Article ID: 1304 - Why does Maestro enantiomerize my structures when I rotate?

Article ID: 1276 - What is Maestro?

Article ID: 1273 - I start a MacroModel computation from Maestro, but nothing seems to happen. The command file (.com) and input structure file (.mae) are written to the current working directory, but there is no log (.log) file, and all of the MacroModel jobs fail. What's going wrong?

Article ID: 1272 - How do I submit distributed MacroModel jobs to a queuing system?

Article ID: 1265 - How do I find information about atomic charges used in MacroModel calculations?

Article ID: 1260 - In the Constrained Atoms panel, I can only modify the force constant and half-width for one atom at a time. How can I adjust the constraint parameters for multiple atoms?

Article ID: 1249 - How do I use LigPrep to prepare structures for Glide?

Article ID: 1246 - What is LigParse and how can I use it?

Article ID: 1243 - What is the structure of LigPrep?

Article ID: 1221 - What are the Schrödinger KNIME extensions?

Article ID: 1213 - I am running Jaguar and want to do a conformational search. How do I do this?

Article ID: 1207 - What scripts are available with Jaguar?

Article ID: 1206 - How do I get Jaguar to work with a batch queue?

Article ID: 1205 - How can I visualize molecular orbitals from Jaguar?

Article ID: 478 - Maestro crashes frequently. What can I do about this?

Article ID: 1471 - What's the difference between Views and Scenes?

Article ID: 1196 - Are there any limitations on Jaguar when run from Chem3D?

Article ID: 1167 - What file formats are supported for dockable ligands in Glide?

Article ID: 1165 - Can Glide be run in parallel — for example on a cluster?

Article ID: 1139 - When using the tautomerizer facility within LigPrep, how can I tell if my structure has a pattern that is matched by the tautomerizer?

Article ID: 1126 - What is a good way to set up a replica exchange calculation?

Article ID: 1109 - I've noticed that the web-based and local BLAST homolog search in Prime give different results. Why is that?

Article ID: 1107 - Does Schrödinger make use of the Dunbrack rotamer library? If not, has Schrödinger assembled a similar library?

Article ID: 1106 - My loop sampling job did not give any results. What can I do?

Article ID: 1104 - I would like to use a site found by SiteMap as input to Glide docking. How do I do this ?

Article ID: 1101 - I ran two Glide docking runs using the same receptor with different constraints and some of my ligands are common between the two docking runs. Is there an easy or automated way to remove duplicate poses from my project table?

Article ID: 1100 - What do I do if Prime Covalent Docking job fails with the following error:

ERROR: Failure in rotatable bond assignment, could not determine relationship between atoms...

Article ID: 1097 - What do I do if Prime refinement jobs on Windows fail with the error:

hetgrp_ffgen.exe-Entry Point Not Found
The procedure entry point gztell64 could not be located in the dynamic link library zlib.dll.

Article ID: 1088 - Can I develop my own KNIME extensions for Schrödinger software?

Article ID: 1083 - Do I need to download KNIME to use the Schrödinger KNIME extensions?

Article ID: 1082 - What components does KNIME include?

Article ID: 1079 - How do I treat open-shell singlets (diradicals) in Jaguar?

Article ID: 1078 - How can I use Jaguar to create and display electrostatic potential and electrostatic density maps?

Article ID: 1071 - When using KNIME, how can I show structures in 2D in a report created with the Report Designer?

Article ID: 1070 - How do I control what's in a KNIME output table?

Article ID: 1067 - Where can I find workflow examples to get started with KNIME and the Schrödinger extensions?

Article ID: 1066 - Where can I find other non-Schrödinger KNIME extensions that I can add to my KNIME installation?

Article ID: 1065 - What are KNIME extensions?

Article ID: 1064 - I have run several related jobs in Jaguar. Is there a way to quickly scan the output files and extract certain numbers?

Article ID: 1061 - Can I do excited state calculations with Jaguar?

Article ID: 1059 - What do I do if Jaguar fails with an error message that includes "The lowest energy configs are degenerate."?

Article ID: 1058 - Why don't the energies I obtained from Jaguar exactly match those from other programs?

Article ID: 1055 - What do I do if the SCF won't converge in Jaguar?

Article ID: 1050 - I previously used a script called align_binding_sites.py. The script gave very nice alignments of binding sites, but I can no longer find it on the Script Center. Is it still available?

Article ID: 1049 - I would like to display the hydrophobic interactions between a ligand and protein. I tried to do this by only showing the good contacts in the Measurements panel (under Tools → Measurements → Contacts in the Maestro menu), but it required me to exclude polar atoms using an ASL expression. Is there an easier way to do this?

Article ID: 1048 - I have read about Schrödinger's Protein Structure Alignment. How can I access this tool?

Article ID: 1047 - How do I restart a failed IFD job?

Article ID: 1044 - How long does it take to run an Induced Fit calculation?

Article ID: 1043 - Why am I getting large positive Prime energies in my Induced Fit Docking run?

Article ID: 1041 - How can I determine whether a side chain of my protein has multiple occupancy or missing density?

Article ID: 1040 - Why are some Maestro panels slow to open?

Article ID: 1039 - What is the default shell size for protein flexibility in Induced Fit Docking (IFD)?

Article ID: 1033 - What should I try if Glide doesn't give me reasonable results?

Article ID: 1032 - Why does Glide produce poses with close intra-ligand contacts?

Article ID: 841 - Sometimes, Maestro fails to start on Windows XP, or I can't run jobs. What's the reason for this?

Article ID: 1491 - I rendered a molecular surface in Maestro using dots, but I feel that the dots are too large. Is there a way to customize the size of the dots?

Article ID: 1488 - How do I extract a tar file or a tar.gz file on Windows?

Article ID: 1030 - What should I do about colored residues in my imported PDB structure for Induced Fit Docking?

Article ID: 1029 - How do I change the residue number for a single atom in a residue, which has the wrong residue number?

Article ID: 1013 - What are the main differences between HTVS, SP, and XP docking?

Article ID: 1010 - Viparr produces an error like: 'In mae file, residue <" ",1> uses multiple names'. What can I do?

Article ID: 1008 - How can I calculate a relative free-energy difference from Desmond mutation by FEP calculations that were run with two different environments?

Article ID: 1005 - Can I run a Desmond FEP job with a fragment that isn't in the list in the Ligand functional group mutation panel?

Article ID: 1004 - Can I use VMD to read and write files for Desmond?

Article ID: 1003 - Can I use other force fields for Desmond simulations?

Article ID: 1000 - How do I start IFD in the Prime stage with preexisting Glide results? I want to include Glide constraints in my IFD run.

Article ID: 994 - How do I generate a list of sequential pK_a values?

Article ID: 993 - How do I limit the number of output structures that Epik generates for each ligand?

Article ID: 988 - Can I use files from other programs, such as Amber, Gromacs, and Charmm, with Desmond?

Article ID: 984 - What other Schrödinger software must be installed to run CombiGlide?

Article ID: 980 - When should I use more bits to generate a fingerprint? There are options for 10-bit, 32-bit, and 64-bit address space. What's the advantage of running with more bits?

Article ID: 979 - Does Canvas support all the standard SMARTS features?

Article ID: 978 - How can I restart a VSW job?

Article ID: 977 - When I try to run a job on Windows, I get an editor window that contains a script instead. What can I do?

Article ID: 976 - I get an error message when I try to unzip a software download. What can I do?

Article ID: 974 - I just installed Schr→dinger software on my Windows machine, but it wasn't listed in the Add/Remove Programs dialog box. What happened?

Article ID: 971 - How do I obtain a license for my Schrödinger software?

Article ID: 970 - I have upgraded my Linux operating system and my older Schrödinger software fails. What should I do?

Article ID: 965 - Will Schrödinger software run on 64-bit platforms under Linux?

Article ID: 964 - Desmond and Jaguar parallel jobs fail when sent to an LSF queueing system. What can I do?

Article ID: 963 - The job I submitted to an SGE queue failed with the status "fizzled". What can I do?

Article ID: 960 - After installing new Schrödinger software, Python doesn't run. Do I need to download and install Python?

Article ID: 957 - How can I use the Schrödinger Python modules with other Python modules?

Article ID: 956 - I would like to filter a collection of molecules and keep those that match a functional group or a SMARTS pattern. How do I do this?

Article ID: 951 - Where should I install Schrödinger software?

Article ID: 950 - How do I search all the manuals for a word or phrase?

Article ID: 949 - Where can I find a list of all the documentation?

Article ID: 947 - How can I obtain an evaluation copy of one or more of Schrödinger's scientific software products?

Article ID: 946 - I have just installed Schrödinger software on my Windows machine. I already have licenses to run the software on another machine, so how do I enable these licenses on my Windows machine?

Article ID: 944 - How do I save scenes in Maestro?

Article ID: 942 - How do I predict the activity of new molecules using an existing Phase QSAR model?

Article ID: 938 - How do I distinctly represent two data sets on the same scatter plot in Canvas, to compare two libraries?

Article ID: 934 - I am running a Glide XP job with default settings, but it is running very slowly. What might be causing this problem?

Article ID: 933 - Does Glide impose a penalty to cis urea ligands? If not, how can I add such a penalty?

Article ID: 929 - While running a Receptor Grid Generation job on Windows, I get the following error message:

zsh:no such file or directory: C:\Schrodinger2009\impact-v55211\bin\WIN32-x86\main1h

Is there a fix for this problem?

Article ID: 928 - Instead of just looking at the GlideScore, I would like to cluster the poses and compare the clusters. Is there a way to do this?

Article ID: 920 - I want to examine the binding of negatively charged sugar chains containing 12-20 sugars (such as heparin) to a target. Can I use Glide to dock these compounds?

Article ID: 918 - When preparing a Glide grid, the native ligand is removed. How do I specify the native ligand as the core to be used for RMSD calculations?

Article ID: 915 - Can I dock a ligand that contains a Cu²⁺ ion?

Article ID: 912 - Where can I find instructions for installing the ActiveX Maestro Viewer Control into PowerPoint?

Article ID: 904 - I am unable to install Suite 2009 on 64-bit Windows Vista. It fails with the message

FATAL: Schrodinger Installer requires maestro-v or GUIDs.ini file

Is there a fix for this?

Article ID: 902 - My Windows installation seems to be messed up. How do I fix it?

Article ID: 1486 - I cannot open some of the Maestro panels on my Japanese Windows XP machine. What can I do?

Article ID: 897 - When I click on some of the toolbar buttons, the menus don't show up. What is the problem?

Article ID: 891 - I want to compare the results of docking a database to several conformers of a target, to find compounds that score well or are ranked well for all conformers. How can I do this?

Article ID: 882 - I'm having problems running the analyze_trajectories.py script from the command line to analyze a Desmond trajectory. Do you have any suggestions?

Article ID: 874 - I would like to run a Desmond mutation FEP calculation on a membrane-bound protein, but the FEP panel does not allow setup with a membrane. How can I do this?

Article ID: 873 - I want to run Maestro on a Linux host and display it to my Windows PC, but it appears that I need an X server. Where can I get one?

Article ID: 866 - After I run a Desmond MD simulation, I want to strip water and counter ions from selected frames in the trajectory file and write them out as separate files. How can I do this?

Article ID: 865 - What's the easiest way to compare a sequence of entries in the Workspace with a reference entry?

Article ID: 859 - I ran a Glide docking job with constraints, but the job failed with the error "unable to allocate floats". What can I do about this?

Article ID: 856 - Can I use proteins from the OPM database to define membranes for these proteins in Desmond or Prime?

Article ID: 853 - The structures that I get back from Epik seem distorted. What can I do about this?

Article ID: 852 - The jobs that I launch on Windows are failing. What might be going wrong?

Article ID: 742 - Wouldn't it be better to have the Schrödinger fragment library available in two versions: one version that is prepared with and one prepared without metal-binding states?

Article ID: 1465 - I have created and exported fingerprints from the Interaction Fingerprints script. Can I use them in the Canvas interface?

Article ID: 850 - When I submit a job to a SLURM queue, I get the following error message:

 
Submitted batch job 555

Submitted batch job 556

FATAL: Unable to submit job for batch execution

Why does the job submission fail?

Article ID: 845 - When I insert or remove a removable disk such as a flash drive on my Windows computer, the drive listing under My Computer doesn't get updated automatically. What do I do?

Article ID: 844 - Can I maintain a single version of the third-party software, such as the PDB, and use it for several Schrodinger releases?

Article ID: 838 - When I move the pointer into the Workspace, it disappears. Why is this?

Article ID: 836 - Some of the Maestro panels don't open on Windows. Is there a fix for this problem?

Article ID: 834 - I'm seeing spacing problems in the Project Table column headings. Is there a fix for this?

Article ID: 833 - When I try to import files in to Maestro, I get the following error:

WARNING : MMDBI ERROR(-4): mmproj_dbi_property_set_dependency():
Failed to execute the prepared statement:PROPERTY_DELETE_DEPENDENCY
error 10 (disk I/O error)

What does this mean?

Article ID: 826 - I am running an IRC calculation with Jaguar, but it is failing. What could be causing this?

Article ID: 825 - For a set of conformers, is it possible to generate an RMSD matrix with the rmsd containing the rmsd between each pair of conformations?

Article ID: 822 - In the output from my Glide docking job, I see these warnings:

%IMPACT-W (warning): At line 58
%IMPACT-W: Extraneous input discarded: MOL 4
%IMPACT-W (warning): At line 59
%IMPACT-W: Extraneous input discarded: MOL 3
%IMPACT-W (warning): At line 60
%IMPACT-W: Extraneous input discarded: MOL 2

What do these warnings mean?

Article ID: 821 - Can I calculate the translational, rotational, and vibrational energies of molecules?

Article ID: 809 - Can I view the parameters assigned by the force field?

Article ID: 808 - If I create a hypothesis manually using Create Hypothesis, how do I add excluded volumes before searching for hits?

Article ID: 805 - If I save more than 1 pose per ligand in Glide, how do I compare the results for a given ligand?

Article ID: 803 - I'm getting the following message when docking a ligand with Glide.

NO POSES STORED FOR LIGAND 1 (******from-structure)
%IMPACT-W: No Ligand Poses were written to external file.

What does this message indicate?

Article ID: 801 - What does the term "Glide rewards" consist of?

Article ID: 797 - How do I submit jobs to a PBS queue?

Article ID: 796 - How do I specify a separate output directory for Glide poses?

Article ID: 786 - When docking a ligand with Glide, I get a warning message:

mmlewis warning: Wrong Lewis structure in structure input file

What does this warning indicate?

Article ID: 785 - How do I dock ligands that contain metals with Glide?

Article ID: 784 - The poses that came out of my Glide docking run did not have a native-like pose. How do I proceed?

Article ID: 782 - The Glide manual reports that for the RMSD only the heavy atoms are considered. Are the hydrogens considered during the calculation of the maximum atomic displacement?

Article ID: 778 - I would like to dock compounds into a large protein, but when I try to generate the receptor grid, I get a message saying that there are too many atoms. How can I prepare a grid for this protein?

Article ID: 776 - Is there a procedure that allows me to systematically place crystal water around a particular residue, for the purpose of docking studies with Glide?

Article ID: 774 - How do I perform docking manually? After I get a pose from Glide, I would like to re-adjust the ligand manually and find out the docked energy for the re-adjusted pose. How can I do this?

Article ID: 773 - When docking in XP mode, how are GlideScore and Emodel used for selecting the best docking pose?

Article ID: 772 - Glide seems to fail to produce accurate docking poses when flexible ligands (e.g. 22 rotatable bonds) are treated. What can I do to get better poses?

Article ID: 771 - I have a lot of protein-ligand complexes, and would like to use Glide SP and XP to calculate the scores. How do I proceed?

Article ID: 767 - Two similar molecules were docked using the same grid. Only their initial conformation were different. Why are the poses generated by Glide for these two molecules different?

Article ID: 765 - Is there a web tool to monitor the use of the Glide web interface - jobs submitted, in progress, finished - and to clean up the jobs directory after the jobs finish?

Article ID: 759 - I have a situation where I want to dock a set of molecules that are atropisomers. The problem I have is that Glide doesn't recognize this and treats the bond as rotatable. What do I do?

Article ID: 756 - Even though I have "sample ring conformations" on, I always get only one conformation of the 5-ring, therefore missing the best docked structure. The input ligand was minimized, which caused the ring to flip to the "wrong" conformation. What do I do?

Article ID: 755 - The core constraints do not seem to constrain the core to where I want it. Is there a way to force Glide to put the core in the right place, and then sort out the rest of the molecule?

Article ID: 754 - Can the per-residue interaction scores at the binding site or the XP descriptors be reported in Excel?

Article ID: 752 - I have been docking a compound with a bond from iodine to an aromatic carbon. The bond length in my minimized input structure is 2.08 Å (matching the crystal value of 2.14 Å), but the output file from Glide had a bond length of 1.55 Å. What's going on?

Article ID: 750 - I would like to use an older version of Glide to run a docking process. How can I designate the Glide version to submit the job?

Article ID: 748 - Is it possible to run the screening of ligand databases with one processor? If so, how much time would it take to complete the screening?

Article ID: 747 - If I were to dock a big ligand like a carbohydrate hexasaccharide, how do I increase size of the inner box?

Article ID: 741 - Can I dock bidentate ligands to a metal ion with Glide, and if so, how?

Article ID: 740 - I cannot seem to kill a job. I'm getting an error message "cannot send the kill command". What might the problem be?

Article ID: 739 - What are the advantages and disadvantages of Glide regular docking and induced fit docking?

Article ID: 729 - I want to dock a molecule with a pharmacophore feature at an active site of an enzyme so that I can see its interaction with the donor and acceptor feature. How can I do this?

Article ID: 726 - Is there a maximum ring size for which Glide is able to generate conformations?

Article ID: 724 - Is there a way I can get an older version of the software back?

Article ID: 723 - How well does Glide deal with binding sites containing metal ions for docking?

Article ID: 722 - In the case of a cofactor existing in the ligand binding site, how do I generate a grid to specify the hydrophobic contact with the cofactor but not the amino acid?

Article ID: 720 - I expected the input and output files from my job to be in the .prj project folder, but they are one level up. Why is this?

Article ID: 715 - I'm having problems docking the Schrödinger fragment library to a protein-RNA complex.The job is encountering a very high rate of ligand rejection (>40% ). Is there anything I could do to rectify this?

Article ID: 714 - I would like to combine 10 pv.mae files. It seems that glide_sort -o writes out the best-scoring poses. However, I want all poses, not just the best-scoring pose files. How do I do this?

Article ID: 713 - I have done XP docking for around 25 molecules and I got the best ten molecules as output. How can I see the docking score for all 25 molecules?

Article ID: 711 - I'm doing a grid generation for a protein with a large and very shallow active site. The ends of some of the residues suspected to be important H-bonding species are outside the box. How can I tweak the box so that those ends are inside and can be used as constraints?

Article ID: 708 - I found that docking to a subpocket and an entire pocket produced different hits. Why would this happen?

Article ID: 706 - Is there anyway to find good-docking compounds that are dissimilar to my known actives?

Article ID: 704 - Is it possible to select one structure from a multi-structure .mae file as receptor input for grid generation? For example, I have a Maestro file containing 100 receptor structures and I want to make a grid for structure number 50.

Article ID: 703 - Is there a way to define constraints such as H-bonds for a Glide command line run, other than using atom numbers?

Article ID: 702 - Is there any way to orient the grid box or rotate the axes of the box so that it matches the shape of the active site?

Article ID: 701 - Could you explain how the size of the grid box affects the Glide result?

Article ID: 699 - I ran a Glide docking job and the Monitor panel indicated that it had finished successfully, but I don't have any results in the Project Table. What's wrong?

Article ID: 695 - I need the Emodel energy of the native poses observed in the X-ray structures. With the "score in place" option, however, Glide calculates only the GlideScore values of the input poses, Emodel scores are missing in the output. Can you explain this please?

Article ID: 694 - In the XP Visualizer, there are ligands for which the H-bond pair term is zero but their H-bond table cell is still enabled and yellow dotted lines are shown on the structure in the Workspace. Why is this? Is it due to a difference between Glide and Maestro definitions?

Article ID: 691 - I want to see the other poses for each ligand, rather than seeing the poses for all ligands in order of GlideScore. How do I do this?

Article ID: 686 - I want to perform docking studies using ligands that contain stable carbenes, but the preparation or docking process changes the carbene atom types. How do I overcome this?

Article ID: 685 - With the van der Waals scaling factor in Glide grid generation, do I have an option to customize the vdW scaling of certain residues in the active site rather than scaling all the non polar atoms in the protein?

Article ID: 681 - Where can I find the _raw.mae file when using the Suite 2009 version of Glide? It isn't in the launch directory when the job finishes.

Article ID: 677 - On browsing the Glide output, I noticed that whilst Glide has calculated Coulombic and polar terms, there are actually no partial charges in the files. Could you explain this?

Article ID: 675 - I used GLIDE_CONS_FEAT_FILE to specify the location of a feature file but $SCHRODINGER/glide seems to be ignoring that keyword. What can the problem be?

Article ID: 674 - Although I select Dock Rigidly from the Glide interface, the poses are distorted. What's causing the distortions in the conformations?

Article ID: 673 - I have an alpha helix which loses its conformation after processing by LigPrep. Is there another way to prepare this type of ligand for docking?

Article ID: 672 - I cannot figure out what some of the XP penalty terms indicate, like the "Blk" penalty. Is there anywhere where these terms are described?

Article ID: 665 - Is it possible to keep a receptor side chain flexible during Glide docking? If so, how do I do this?

Article ID: 662 - At times, I get no docking results when using SP but get some good-looking poses when running XP. Why does this happen?

Article ID: 655 - In the log file, although 10 ligands were docked with none failing, only 4 were written out. Why would this happen?

Article ID: 654 - At what point in the Glide docking process is ligand torsional sampling done?

Article ID: 653 - Is there a paper on the methodology of Glide?

Article ID: 649 - How do I define the active site for Glide grid generation if I don't have a ligand?

Article ID: 648 - Do I have to create a new grid for each ligand I attempt to dock?

Article ID: 645 - I am trying to set up a Glide grid with an H-bond constraint. When I click on the side chain N of Lys, Maestro says "WARNING This type of atom cannot be used as a Glide constraint". How do I add it as a constraint?

Article ID: 640 - Do I have to minimize the ligand conformation with third-party tools such as MOPAC or Gaussian before I do a docking run?

Article ID: 636 - Is there any way to change the protonation states for residues in the active site when preparing the Glide grid? For example, if I want to have a tyrosine in a deprotonated state, how should I do this?

Article ID: 633 - How is the GlideScore calculated?

Article ID: 629 - Is there a way of running ConfGen to generate a big pool of conformers for a certain molecule with a distance constraint?

Article ID: 628 - Is there any way I can add my own ring templates to ConfGen or Glide?

Article ID: 626 - How long does a ConfGen job usually take?

Article ID: 625 - How are compact conformations removed by ConfGen?

Article ID: 623 - How can I calculate the volume of a molecule?

Article ID: 621 - What is the unit of potential energy in the output from Confgen standard?

Article ID: 617 - How do I assign training and test sets in Canvas model building applications?

Article ID: 616 - How do I run a ligand preparation and filter the results by Lipinski's rules?

Article ID: 613 - I am interested in the interaction of one drug molecule with another drug molecule. Can I dock a ligand to another ligand with Glide?

Article ID: 612 - I am working on a system in which the ligand forms a dimer. Can I dock ligand dimers with Glide ?

Article ID: 608 - I was running some Glide dockings over some relatively large ligands when the output showed repeatedly a warning saying 'TOO MANY PATOMS IN BOX.'

What does this mean?

Article ID: 606 - Is there a way to get information about the bad contacts, after Glide docking?

Article ID: 605 - Where can I find information about how to submit jobs to a cluster?

Article ID: 602 - I find that it takes a long time to dock 50 compounds in Glide XP. What can I do to complete this in a short span of time?

Article ID: 599 - Would it be better to perform blind docking before proceeding with grid docking?

Article ID: 595 - My distributed Glide XP job failed when one subjob yielded no poses. How do I fix this?

Article ID: 592 - I am not able to click on the Edit Feature button in the Constraints tab of the Ligand Docking panel - is this feature not available to me?

Article ID: 590 - I've been running some Glide XP jobs and they crash with the same error.

%IMPACT-E (die): At line 69
%IMPACT-E: Insufficient storage for pointers. Pointer set at 1501

What is going on?

Article ID: 589 - Is there any way to stop or kill a 'Stranded' Glide docking run but still recover any docking results and scores that were completed?

Article ID: 588 - I am learning how to use Glide for molecular docking. Where can I find a manual for Glide?

Article ID: 584 - The Astex Diverse Set published in 2007 (J.Med.Chem, 50, 726-41) is intended for the validation of docking software. Can I assume that most of its complexes are used in the parametrization of Glide?

Article ID: 578 - Why does Maestro crash when I run it on a VM?

Article ID: 577 - What does the following error message from a Glide docking run mean?

NO VALID POSES AFTER MINIMIZATION:SKIPPING.

Article ID: 570 - I need to define a constraint based on distance between the ligand and a few residues. Would it be possible to create this constraint and add a potential?

Article ID: 568 - When combining the results from an ensemble docking into one pose viewer file, what is the significance of the GlideScore offset?

Article ID: 567 - Is there a way to see the per-atom contribution to the docking score?

Article ID: 563 - Is it possible to score an interaction between protein and ligand given by other software (e. g., a MacroModel optimised structure) using the Glide scoring function?

Article ID: 558 - I would like to use some of these keywords but the explanation in the Glide manual is not clear to me. Could you please provide me with some more information?

ASLSTRINGS list
GLIDERECEPTORSCALECHARGES list
GLIDERECEPTORSCALERADII list

Article ID: 557 - Why is the Glide pi stacking term always zero?

Article ID: 556 - Is it possible to specify an aromatic ring positional constraint in Glide? Also, is there a default aromatic ring SMARTS pattern, or can one edit the patterns in the hydrophobic features to choose only aromatics?

Article ID: 554 - I seem to have a problem with KNIME. I am using the partitioning node to run separate jobs. Some of the nodes were shown as queued. However, only four nodes were passed. What's causing this?

Article ID: 552 - How do I pick two different lowest energy torsion conformations from the Rapid Torsion Scan panel and add them to the Project Table?

Article ID: 550 - I seem to be getting wrong charges for carbon atoms (charge 0) when I have unusual multiple ring systems. Is there a way around this problem?

Article ID: 548 - Was OPLS_2005 in Schrödinger primarily designed for simulations in water? Can it be used for nonaqueous solvents as well?

Article ID: 544 - I want to run a CHARMm computation and need to write a force field parameter file for the ligands that I have. Does the Schrödinger package have a feature for this?

Article ID: 541 - I am trying to dock a ligand with free radicals to a receptor using OPLS_2001 with Glide but I don�

Article ID: 540 - Does MacroModel modify the values of epsilon, sigma or partial charge during single point or energy minimization calculations?

Article ID: 538 - Frequent folder refresh is causing slow performance with large (>10,000 files) NFS folders. Is there a way to adjust the refresh interval?

Article ID: 535 - I have run the flexible alignment tool and it overlays the molecules nicely however it doesn't update the Project Table. Therefore when you exclude one molecule you lose the alignment. Is there a fix for this?

Article ID: 532 - The job launch panel allows for the input of the username. Why would this be needed?

Article ID: 528 - Display of 3D surfaces causes Maestro to freeze. Sometimes, after creating a surface, it can only display as mesh or dots, but not as a solid surface.

Article ID: 519 - I am interested in structure-based modeling of GPCR receptors. How should I apply Schrödinger software to this task ?

Article ID: 517 - Ever since I installed Suite 2009 update 1, I find that I cannot import molecules from Spartan. I get a

"WARNING Could not open file for importing"

message. How do I do this?

Article ID: 514 - I was trying to save to PDF from the 2D Viewer panel when this error appeared in the terminal. What is the problem?

/software/schrodinger/mmshare-v18109/lib/Linux-x86/lib/python2.6/site-packages/reportlab/pdfbase/pdfutils.py:44:
SyntaxWarning: assertion is always true, perhaps remove parentheses?
assert(len(raw) == imgwidth * imgheight, "Wrong amount of data for image")

Article ID: 513 - When I use a Boolean operation in the Molecular Surface panel, I find that selecting "Low image quality" and "Surface Context: Selected Atoms" produces a reasonable map, however changing the quality to medium causes it to crash. The warning message I get is

WARNING check_residue: no template for residue 903 (BMA ), chain 'A'.
WARNING check_residue: no template for residue 951 (PGE ), chain 'A'.
/usr/schrodinger/maestro-v85207/bin/Linux-x86/startup: line 984: 32449 Segmentation fault

Article ID: 505 - Maestro either freezes or crashes when I try saving an image. What can I do to prevent this? Also, if I do save the images,they are either distorted or get saved in black and white. How do I save them?

Article ID: 503 - How does the Title field in Maestro get filled in? At times, it's the file name. Is there a way to set it such that the file name becomes the title by default?

Article ID: 501 - Is it possible to color-code the Connolly (molecular) surface by calculated hydrophobicity?

Article ID: 490 - I notice a considerable speed lag with Maestro, on a dual quad core machine, when running QM jobs in the background. All of the processes are running on the quad-core Red Hat: Maestro, QM job on single processors and rdesktop session to the Windows machine. What's causing the lag?

Article ID: 485 - How do I visualize a Desmond trajectory in Maestro?

Article ID: 480 - I would like to view an MD trajectory generated by Desmond while the simulation is still in progress. I loaded the jobname-out.cms file into the Maestro Project Table. When I clicked the "T" button, a message regarding a missing trajectory file jobname_trj.idx appeared. When I tried to import the file with the "Import File" button, Maestro crashed. What is the problem?

Article ID: 474 - How do I to connect to a client machine from a server? I'd like to run Maestro on the client machine but remotely from the server.

Article ID: 473 - I have a samba share configured and can access *.prj.zip projects. However , I cannot seem to access a normal uncompressed *.prj project on my Linux share. Is there a way to get the PC Maestro configured to read the Linux projects?

Article ID: 472 - I can't seem to be able to move the ligand independently of the complex. I have both the metal center and a ligand in the Workspace but I see only one entry in the Project Table. How do I do this?

Article ID: 470 - I found that Protein Reports reported a steric clash between residues on opposite sides of the protein. Is this an issue?

Article ID: 469 - I have a project with 16 entries containing surface plots. I want to display all 16 molecules together in the Workspace in a grid-like fashion so that I can visually compare the plots (molecular orbitals) side by side, and output an image file to incorporate into a PowerPoint presentation. How do I do this?

Article ID: 466 - Is there a way to export a 2D SD file from Maestro?

Article ID: 465 - Is there a command-line script to generate a PDF file from SD structures, similar to the 2D Viewer Export functionality?

Article ID: 462 - I am running Maestro 9.0 natively on Windows XP and locally. Im thinking of upgrading to a quad core processor. Does the software use all four cores?

Article ID: 460 - Is there a way I can assign a free radical atom type for oxygen in the Build panel? I want to create a tyrosyl free radical.

Article ID: 459 - I run Maestro on a two monitor system. When I move a new Maestro panel over to the second display its graphic area becomes filled with random pattern of coloured squares. The error message I get is:

WARNING MM_Primitives::FATAL!! d_circle_list is ZERO!
WARNING no error 0
WARNING MM_Primitives::FATAL!! d_sphereh_list is ZERO!
WARNING no error 0

The video card I use is a Matrox Millenium P650 PCIe 128 card. What's going wrong?

Article ID: 455 - Is Maestro supported on Windows 7 or Windows server 2008?

Article ID: 1483 - Does Schrödinger have a statistical method that can categorize compounds or build an activity model based on decision trees?

Article ID: 1176 - What do Glide pose-rejection messages mean?

Article ID: 449 - Is it possible to define an ASL where you can superimpose A-->B and C-->D?

Article ID: 447 - I see a message "WARNING The PDB file 'pdb1t64.ent' can not be located in the database. See the on-line help for suggestions about how to make it available for use as a template." What does this indicate?

Article ID: 444 - I find that the mouse does not seem to work with Maestro although it works just fine outside. Is there any setting I need to change?

Article ID: 442 - I want to attach a customized label to entries in my Project Table. How can I do this?

Article ID: 440 - When I resize the Start panel, the size of the panel goes back to its original size the next time I launch. Why does that happen?

Article ID: 438 - After installing a new release, I found that Maestro didn't seem to work: it failed with FATAL error messages. What's causing the problem?

Article ID: 436 - How do I get a nucleic acid ribbon representation?

Article ID: 434 - Is there a way to export pdb files that include the records HET, HETNAM, FORMUL from Maestro?

Article ID: 433 - After a conformational search of a molecule, is there a way to add to the Project Table a column of some measurable values, such as an H-bond distance or a torsion, so that it can be plotted for some statistical study?

Article ID: 432 - If I run a Glide job from Maestro and switch to another desktop to do something else while the job is running, it automatically switches back to the original desktop when the job completes. How can I stop this?

Article ID: 430 - How do you move molecules independently in Maestro?

Article ID: 429 - I would like to map a water network in Maestro for a picture but I do not want to display the distance values, nor the hydrogens involved in the network, just the dotted black lines. Is there a way to do this with Maestro?

Article ID: 426 - How can I import extra data for the structures that I have in the Project Table?

Article ID: 425 - I seem to have a problem with rotating and moving the molecule with the wireless Logitech mouse that I have. This is a three button mouse but the middle one is a wheel. What can I do about it?

Article ID: 424 - I have renamed some of the columns in the Project Table. When I export an SD file from this table, the fields in the SD file have the original names, rather than the new names I have given them. Is there a fix for this problem?

Article ID: 423 - Where can I find a user manual for your software? Can I download it?

Article ID: 421 - Does Maestro handle symmetry? The symmetry information is defined in the .cms file created by Desmond.

Article ID: 420 - I have several similar proteins aligned, and I'd like to see them in a sequence viewer which displays residues and shows which ones are matched, as in typical sequence alignment output. How do I do so?

Article ID: 419 - What are the operating systems supported by Schrödinger?

Article ID: 418 - Is it possible to type in a filter to show only a subset of the files in the file selectors in Maestro?

Article ID: 417 - Do you have a utility to clean up a PDB file? I have some PDB files with just simple atom names C, N, O, H instead of unique atom names and Maestro seems to be modifying their names.

Article ID: 415 - How do I assign PDB atom names?

Article ID: 412 - Is there any sort of copy/paste tool I can duplicate the structure in the Workspace?

Article ID: 411 - How can I generate a dimer from a given conformation of a monomer?

Article ID: 409 - Is it possible to convert an .sdf file into an .maegz file from the command line?

Article ID: 406 - Is there a way to turn off the depth / perspective filtering so that as you rotate things everything is always visible?

Article ID: 405 - Is there a way to reset or redefine the center of rotation of the current molecule on the display?

Article ID: 402 - How can I load the electron density of a protein from x-ray crystallography data?

Article ID: 401 - How do I calculate torsions after a conformational analysis of a single compound and write the data into a table?

Article ID: 399 - Is it possible to transform molecular coordinates, so that, for example, all Z coordinates are nearly zero (for a planar molecule)?

Article ID: 398 - Is there a way to visualize the coordinate system and dipole moment components in Maestro?

Article ID: 397 - I have a file of protein residue properties which I'd like to color-map to the protein surface. Is this possible in Maestro and if so how do I do it?

Article ID: 396 - How do I change the Workspace background color to white?

Article ID: 395 - How do I save an image in Maestro?

Article ID: 393 - I have chirality displayed in my ChemCart dbase entry for a molecule (wedged/hashed bonds). I export the .mol file and import it into Maestro, but the molecule comes in flat. How do I import the molecule so that the chirality of the dbase entry is maintained?

Article ID: 390 - I get the error

"application failed to start because python25.dll was not found. Re-installing may fix it "

Is there a solution apart from re-installation?

Article ID: 389 - How can I access the online help?

Article ID: 388 - Can I superimpose molecules that are "selected" rather than those "included" in the Workspace?

Article ID: 386 - Can I export Project Table data in ASCII formats such as csv or txt, so as to take the project table data to MS Excel (for example) for presentation or further analysis?

Article ID: 385 - Is there a way I can write brief notes on each project?

Article ID: 381 - Can I "mark" entries in the Canvas project?

Article ID: 378 - When trying to start Maestro on Fedora 9, we got the following error message. What can we do?

error while loading shared libraries: libX11.so.6: cannot open shared object file: No such file or directory
Maestro: Could not load shared library

Article ID: 367 - How can I add a column in the Project Table that shows a count of the H-bonds for all my entries?

Article ID: 365 - In the Project Table, is there a way to re-assign one of the compound properties as the compound title?

Article ID: 364 - There are four torsion sampling options in a MacroModel conformation search. What is the difference?

Article ID: 363 - What are the Molconn-Z Estate molecular descriptors found in Canvas?

Article ID: 362 - Can I count the number of chiral centers in my collection of molecules? Can I filter on the number of chiral centers?

Article ID: 358 - Can the Protein Preparation workflow be run from command line?

Article ID: 356 - Is it possible to assign bond orders to PDB ligands from the command line?

Article ID: 355 - I want to see only the top pose for each ligand from a Glide docking run, and step through these poses by ligand. How do I do this?

Article ID: 354 - Can I prepare a video file for incorporation into PowerPoint showing some modelling results?

Article ID: 353 - Maestro projects sent to compressed zipped folders on Windows XP are incomplete and cannot be opened. What should I do?

Article ID: 350 - Is there a way to selectively hide columns that are not relevant in the Project Table?

Article ID: 346 - How do I view alternate positions of residues such as Arginine?

Article ID: 345 - When I first import a PDB structure, what do the different colors mean?

Article ID: 343 - How do I selectively rotate or translate a ligand within its binding site? I want to manually dock the ligand.

Article ID: 341 - How are LigPrep and Confgen different in the way they prepare ligands? Do they do the same thing?

Article ID: 340 - I am using LigPrep to prepare 3D ligands for modeling. How do I generate only a single output structure per input structure?

Article ID: 336 - Is there a way to figure out specifically which compounds to buy from one library to supplement another? I need to decide if I want anything from a second library (external collection) to complement the first (internal collection), pick the ones I want, and output them as an sdf. Is this possible?

Article ID: 335 - Can I perform a minimization on my structure keeping the bond torsions fixed? Just the bond lengths and angles would be optimized.

Article ID: 334 - Can I associate distinct strucutural features with the individual bits in a Canvas fingerprint?

Article ID: 332 - I have a file of structures, and I would like to generate a subset of structures. What methods are available to me?

Article ID: 330 - Where can I find the library of standard PDB structures?

Article ID: 323 - How do I make Embrace faster ?

Article ID: 322 - Can I obtain minimized structures from MacroModel dynamics simulations?

Article ID: 321 - I have the cas number of a ligand, and I would like to generate a 3D structure. How do I do this with Schrodinger software ?

Article ID: 320 - I see that SiteMap has a druggability score. What is it, and how is it different from the SiteScore?

Article ID: 319 - Why are structures that have residues ARN, ASH, GLH, LYN, HIE, HIP incorrectly changed to ARG, ASP, GLU, LYS, HIS when converted to PDB?

Article ID: 310 - What can I do if IFD dies in the Protein Preparation stage? There is a warning:

Expected output file _rec-1_ref.mae not found.

and the jobname_rec-1.log file in the jobname_workdir/ directory has this message:

** Final rmsd is greater than 0.18. No output structure is saved.
Increase the rmsd limit via [-r rmsd] and run refinement again.

Article ID: 309 - Are water molecules flexible in IFD?

Article ID: 307 - How is the IFD Score calculated and what is its units?

Article ID: 306 - Is it possible to include more than one loop to sample in the IFD protocol?

Article ID: 305 - There is a loop close to the active site of my system. Can I sample it as part of the IFD protocol?

Article ID: 304 - How can I disable ring sampling during the docking stages of IFD?

Article ID: 302 - Is it possible to perform a Jaguar calculation on a molecule containing deuterium? D is not one of the elements listed in the Atom Properties table, and I'm not sure how I'd set an atom to be D in the .in file.

Article ID: 301 - How can I automate binding site MD with a truncated protein?

Article ID: 299 - Which force fields are available in Desmond?

Article ID: 291 - I want to use multiple trajectories in the Simulation Event Analysis script to analyze a Desmond MD simulation. Is there a way I can combine multiple trajectories for use with the script?

Article ID: 285 - I am trying to rotate all the molecules in a Maestro Project Table by 90 degrees and store the updated coordinates in the Project Table. Although the script rotates the molecules in the project, it does not save the updated coordinates to the Project Table. What can I do to change this?

Article ID: 284 - How can I check the status of all jobs in different job databases, like the one made by the installation check command $SCHRODINGER/run installation_check.pl -testall

Article ID: 283 - How can I do a quick performance check of how fast and reliably my cluster can generate a large Phase database?

Article ID: 282 - I use a Linux license server and have problems accessing the licenses on clients. How can I check if a firewall is causing these problems?

Article ID: 279 - I have a large LigPrep job distributed over several CPUs and subjobs, which seems to hang. How can I get the results for the prepared ligands that have been processed so far?

Article ID: 277 - Trying to visualize Desmond trajectory is causing Maestro crashes when I click on the "T" button next to the _desmond_scratch_donotchangeN entry. What am I doing wrong?

Article ID: 276 - How can I continue with the "Analyze Library" stage in the CombiGlide GUI after running the "Dock Library" stage from the command line?

Article ID: 275 - Launching Maestro opens Notepad instead with some script. What should I do?

Article ID: 274 - In loop prediction, by default, side chains within 7.5 Å from the loop are refined. What is the basis for the selection of the side chains?

Article ID: 270 - The error I am getting in Maestro when I enable stereo is:

WARNING: Hardware stereo is not available.

What can I do to fix it?

Article ID: 267 - I would like to know whether it is possible to export all the entries of a Maestro project in a series of different PDB files, and if so, how?

Article ID: 264 - What is the meaning of increasing R-squared and Q-squared values with increasing number of PLS factors?

Article ID: 262 - Is there any command-line methodology to construct a QSAR model for an alignment generated by a third party program, without doing hypothesis creation by Phase?

Article ID: 257 - Is there a way to generate a Phase subset directly from a database matches file?

Article ID: 254 - What does the 'stability' of a QSAR model mean, and how is it calculated?

Article ID: 251 - How do I calculate the binding site volume and report the result in Å³ in Maestro?

Article ID: 1432 - How do I rotate structures in Maestro?

Article ID: 250 - How do I calculate the surface area of the active site's Connolly surface?

Article ID: 248 - What does it mean that Jaguar stopped with the following error message in the jobname.out file?

** Jaguar license is missing **

Article ID: 247 - I see that the new tile function in Maestro 9.1 creates multiple Workspaces. How can I make Maestro do what the old tile function used to do, which is separate all included entries by modifying the coordinates?

Article ID: 241 - Is there a way for maesubset to skip the N last structures?

Article ID: 239 - Do you have a table in which Lennard-Jones parameters of OPLS-2005 force field are given?

Article ID: 233 - How can I view the Fukui indices that I calculated with Jaguar?

Article ID: 232 - I have a congeneric series of compounds I would like to dock with Glide, but I want the common scaffold of the ligand series to always dock into the same position - I want it to have the same scaffold position as the lead compound does in my crystal structure. Can I do this with Glide?

Article ID: 230 - My colleague and I would like to share our Maestro projects. What is the best way for us to do that?

Article ID: 229 - During a Macromodel torsion scan, it minimizes my ligand at each stage of the torsion scan. How can I do a rigid torsion scan using Macromodel?

Article ID: 1398 - What is the science behind QikProp? How does the program work?

Article ID: 989 - How can I create a CMS file that can be used in Desmond from a file that contains the entire system, including solvent?

Article ID: 228 - I drew a ligand in the Maestro workspace, and my colleague did the same. We ran them through LigPrep and Glide docking and got different results! What is happening?

Article ID: 224 - What does the warning I get on startup of Maestro mean?

Warning: The action Id main_script_ Renumber proteins by 3D alignment cannot be added as it already exists in the map

Article ID: 216 - I would like to select a set of 100K-200K new compounds (from vendor libraries) that are diverse with respect to each other and also diverse with respect to the compounds we already have. How should I do this?

Article ID: 215 - For scatter plots, heat maps, and model building, can Canvas automatically transform activity data into logarithmic data ?

Article ID: 212 - Can I use QM/MM to calculate a protein-ligand binding energy? I would like to treat the ligand quantum mechanically and the receptor with the OPLS forcefield.

Article ID: 206 - Is it possible within Phase to work with pre-aligned ligands?

Article ID: 198 - I tried to calculate ESP charges in QSite but the atomic charges did not change. What should I do?

Article ID: 197 - What is the small down-arrow on the Maestro tool bar buttons? When I click the button, nothing happens.

Article ID: 186 - What type of constraints can I use with Glide?

Article ID: 180 - How can I easily dock a library of homologous molecules?

Article ID: 179 - I often mess up project table entries, which is frustrating, and find that I can't undo the changes. Is there a solution?

Article ID: 178 - How can I view sequence variations in the context of a 3D structure?

Article ID: 170 - How can I inspect the files generated by a node and rerun the same calculation through the command line (e.g. for debugging purposes)?

Article ID: 167 - I did a redocking calculation using Glide with a relatively large ligand. One part of it fits perfectly compared to the reference, the other part does not. Why did Glide fail to predict a fully correct binding mode?

Article ID: 166 - I performed a Glide docking calculation but the results do not appear in my Project Table. What do I do?

Article ID: 165 - I selected a few atoms within Maestro and clicked on a button, e.g. to change their color or representation, but nothing happens. What did I do wrong?

Article ID: 164 - I am converting smiles strings or 2D structures to 3D structures with LigPrep. How does LigPrep treat 1,4-disubstituted cyclohexanes ?

Article ID: 161 - What ribbon-fitting algorithm does Maestro use, and in what cases does the ribbon position track that of CA atoms?

Article ID: 157 - I have built my GPCR homology model but I can't find a residue that a publication refers to using the Weinstein-Ballesteros numbering. Is there a way to renumber my structure using this scheme?

Article ID: 149 - Some of my jobs died when submitted to the queue on my cluster because there are not enough licenses when the job starts running. Can I do something to prevent that?

Article ID: 147 - I would like to keep my input, output, and log files in my project. Is this possible?

Article ID: 141 - How can I display the structures of a Maestro column in 2D, in Knime?

Article ID: 138 - How do I get started with Python scripting?

Article ID: 136 - When I used the hbond analysis in Simulation Event Analysis tool, I picked the hydrogen bond donor and acceptor atoms and the plot showed 0 hbonds although I am sure there is a hydrogen bond. What is wrong?

Article ID: 133 - Is there a way to generate a hypotheses from a set of pre-aligned structures without having to go through the entire Develop Pharmacophore Model workflow?

Article ID: 132 - Is there a way to superimpose common features of two hypotheses a create a single new hypothesis?

Article ID: 128 - Could you tell me a bit about installing Schrödinger software on a cluster? What is required?

Article ID: 127 - How is the Phase screening process performed when the feature tolerances are not set?

Article ID: 121 - During relative binding FEP, I am getting a very high dE energy for a lambda window. Why is this?

Article ID: 119 - I want to calculate the interaction energy between a residue and another chain in a protein/antibody. What program or script can I use?

Article ID: 117 - I want to connect a fragment to a protein without moving them in space. When I use 'Connect and Fuse', it moves them. What should I do?

Article ID: 111 - What is the easiest way to do a quick minimization of a ligand that I build in the Workspace?

Article ID: 109 - What is the most efficient way to quickly browse through the results of my Glide docking calculation?

Article ID: 107 - I have cluster nodes with two Intel Westmere 6 core CPUs and a PBS-like queuing system. How should I configure my schrodinger.hosts file for parallel applications like Desmond?

Article ID: 105 - I only have a few Desmond licenses, but I want to run FEP jobs. I keep getting error messages about unavailable licenses. What should I do?

Article ID: 102 - I imported a receptor and ligands into Maestro and started a MacroModel Embrace calculation. A jobname.com file was generated in the working directory, but no computation was started and no output structure files were produced. What could be the reason?

Article ID: 100 - Can I filter a collection of compounds based on REOS rules ?

Article ID: 97 - When I perform an NBO calculation in Jaguar, some of the output files seem to be missing. Why is this?

Article ID: 96 - Using MacroModel, I receive an error message that includes the phrase "could not ALLOCATE". What does it mean, and what can I do?

Article ID: 95 - Using Canvas, can I run fingerprint generation from the command line, and import the resulting fingerprints into the user interface ?

Article ID: 94 - When running a script from the Schrödinger Script Center, I recieve an error message with the line "Name 'panel' is not defined". Why ?

Article ID: 93 - Can I export structures from Canvas in 2D coordinates?

Article ID: 92 - I would like to perform smiles to 3D conversion, maintaining the title field in the output structure file. How do I do that?

Article ID: 91 - I'd like to perform a mutation via FEP, but the fragment I want is not listed in the fragment library. Can I still perform the mutation?

Article ID: 89 - How many Bayes categories should I use?

Article ID: 87 - What stereochemistry options exist when converting from 1D/SMILES or 2D to 3-dimensional ligand-like structures?

Article ID: 86 - Can I filter my compounds based on ADME properties ?

Article ID: 85 - How do I cluster my ligand-like compounds, and choose a representative sample of each cluster ?

Article ID: 83 - How do I generate 2D sdf files from my 3D structures ?

Article ID: 82 - I would like to add restraints to my relative FEP calculation. How can I do that?

Article ID: 81 - My cluster contains a mix of x86 and x86_64 compute nodes. Sometimes, my jobs get stuck in the 'submitted' status and never seem to run. What could be happening?

Article ID: 80 - How can I add my data to the Maestro Project Table ?

Article ID: 78 - Something went wrong with my job, and it is lost on a remote host. How do I get my results back?

Article ID: 74 - I'm running a Desmond multisim job, and would like to monitor Desmond's .log file and .ene files while the job runs, but they are not in the launch directory. Where can I find them?

Article ID: 73 - My job fails to start and I see error messages like:

12Couldn't read jserver port. Retrying....
12 can't open jserver PID file /home/user/.schrodinger/.jobdb/jserver.host.pid

What does this mean?

Article ID: 72 - In LigPrep, there are options to generate ligand states using either Ionizer or Epik. What is the difference between the two, and how do they affect downstream Glide results?

Article ID: 70 - Can I perform NBO calculations with QSite, or are they only available with Jaguar ?

Article ID: 62 - What does it mean if the docking stage in IFD fails with the following atom overlap error?

%IMPACT-E (die): At line 11
%IMPACT-E: CREATE: atom overlap found in struc file

Article ID: 60 - How do I run extended loop sampling or cooperative loop sampling jobs from the command line?

Article ID: 55 - How can I best display the spin density for a structure after performing a QM calculation?

Article ID: 53 - How can I keep the documentation index page open when I click a link to look at a document?

Article ID: 50 - It took quite a long time for my website account to be activated. Why is that? Is the activation automatic or is each one done manually?

Article ID: 46 - The installed Schrödinger software contains 'blast'. We would like to use this application but we need to know if this is NCBI or WUBLAST as we will need the appropriate databases for it.

Article ID: 41 - In a Jaguar calculation does the Solution Phase Energy contain the Solvation Energy or is it the internal energy of the solute in the solvated phase?

Article ID: 38 - In QSite calculations it is common to have a receptor treated with MM and a ligand treated with QM. Can I treat only part of the ligand with QM?

Article ID: 36 - What are the docking settings used in CombiGlide core hopping that I can use to reproduce the docking results in Glide?

Article ID: 35 - Can you comment on the usefulness of running only the alignment part within CombiGlide core hopping and then using the dressed library for docking within Glide?

Article ID: 33 - I would like find matches on at least 2 of n sites, where n ≥ 3, but Phase only allows matches on at least 3 of n sites. Why does Phase require matching on at least 3 sites?

Article ID: 30 - How can I save a publication-quality image in Maestro that meets most journal submission requirements?

Article ID: 29 - What is target preparation and why is it important?

Article ID: 27 - What is the DockingScore and how do I use it?

Article ID: 21 - How can I combine two Desmond trajectories?

Article ID: 14 - I ran a multi-stage Desmond job using the multisim utility. Where can I find the output structures from all the intermediate stages of my Desmond simulation?

Article ID: 10 - When running Jaguar or QSite calculations, I obtain the following warning in the log file. How can this be avoided?

libibverbs: Warning: RLIMIT_MEMLOCK is 32768 bytes.
This will severely limit memory registrations.

Article ID: 7 - Can Maestro visualize electron density maps? What file formats are supported?

Article ID: 1480 - I am trying to run Schrödinger software on a system that has special characters in the standard Windows paths (non-English locale), but my jobs are failing. What can I do about it?

Article ID: 1479 - I'm having trouble docking a native ligand into the binding pocket of a metal-containing receptor. I find I need to add a hydrophobic constraint for a solvent-exposed phenyl ring. What might be the problem?

Article ID: 1103 - Does Schrödinger have any tools available to help with the identification of crystallographic waters?

Article ID: 923 - Can I use constraints to speed up a Glide docking run?

Article ID: 764 - I am having trouble configuring the Glide Web Interface, using the Apache server that comes with the OS. What do I need to do to get it to work?

Article ID: 760 - Do you have any documentation for the new Ligand Interaction Diagram script from the Script Center? What do the different colors mean?

Article ID: 746 - How do I know if the input file for Glide is the simplified version or not?

Article ID: 743 - How do I determine if a particular ring is included in the template library?

Article ID: 727 - Is it possible to generate your own ring template conformations for Glide to use?

Article ID: 698 - I would like to export all the information in the Glide pose viewer file as a text file or excel file so I can use it in a spreadsheet. How do I do this?

Article ID: 693 - LigPrep prepared my ring compounds in the equatorial conformation. However, after performing docking with Glide XP (with one pose per ligand), the compounds were in an axial conformation. Is there a reason for this?

Article ID: 688 - Is there a way to apply a positional constraint when using the Glide web interface?

Article ID: 687 - If I do not select 'Use input partial charges' for my ligand does Glide automatically assign them before docking?

Article ID: 684 - In the Protein Preparation Wizard, what exactly are the "treat metals" and "metal mode" options?

Article ID: 679 - In Glide, I would like to be able to set certain torsional constraints in my ligand. Is there a way to do so?

Article ID: 671 - How can I cluster ligand poses generated by Glide, within a root-mean-square-deviation of 2.0Å?

Article ID: 658 - Is there a script that highlights or lists the most relevant contributions (electrostatics and van der Waals) to the interaction between a ligand (given pose) and the active site residues? I'm interested in the ligand pose results from long MD simulations, followed by energy minimization.

Article ID: 619 - I notice that some of my molecules failed to have their properties generated by QikProp. How do I tell which input molecules failed?

Article ID: 611 - When I try submitting a job the following error appears:

Error: -NJOBS option only available with simplified docking jobs

What does this mean?

Article ID: 591 - Is there a way to perform a Glide calculation with water molecules? How do I take into account the possible movement of the water molecules?

Article ID: 510 - I did a protein alignment and the windows showed the results such as RMSD etc. However,I can't seem copy the results. What do I do?

Article ID: 536 - If other independent windows are moved across the Maestro main window (in any way) their image remains there until I click in the main window. What's causing this issue?

Article ID: 526 - I am trying to run a blast search from the Multiple Sequence Viewer in Maestro 9.0.211. The job fails with the error:

"Cannot run the job. Please make sure you have installed third party components"

What do I have to do to get it to work?

Article ID: 520 - I am using Maestro 9.0 and am unable to edit the calculated values for 'QM Energy' as calculated from Jaguar. What do I do?

Article ID: 515 - When the Status Bar is displayed at the bottom of the Maestro window and saving of project changes is set to "only when specifically requested", then the Status bar changes in size as the floppy disk icon appears or disappears based on how the mouse is used. This causes the structure in the display window to get re-sized. Is there any way to prevent this?

Article ID: 512 - On Windows, I find that Maestro 9.0 crashes when I try Glide docking. How can I prevent this from occurring?

Article ID: 506 - I just started using macros in Maestro. They initially worked but now Maestro crashes every time I use a macro from the Scripts menu. What is the problem?

Article ID: 499 - I cannot duplicate or split an entry in the project table, and I get the following error. What is the problem?

WARNING : MMPROJ ERROR(-4): priv_mmproj_table_pundo_write():
Can't save copy of filename for undo: errno 18
Invalid cross-device link

Article ID: 495 - Is it possible to turn off the display of the labels on illustrations of pharmacophores?

Article ID: 491 - How can I improve the quality of the images exported as PDF from the 2D viewer?

Article ID: 482 - When I open the manuals index with Adobe Reader, Maestro crashes. Some of the other options such as the Python Module Overview and Python API links don't function. Is there anything I can do about it?

Article ID: 463 - Maestro gives an error saying that 3D stereo is not available. I tried to install the latest driver for my graphics card but it failed, complaining about XEN. Turning that off enabled compilation of the driver but the 3D does still not work. Any suggestions?

Article ID: 461 - How do I place a single atom in the Workspace?

Article ID: 453 - Can we use rsh in our internal network connection, rather than ssh without password?

Article ID: 394 - Where do I find the Build toolbar? I want to be able to add bonds between atoms and add a hydrogen or two.

Article ID: 325 - How do I import multiple surfaces (.vis files generated by Jaguar or SiteMap) and associate them with a structure?

Article ID: 308 - I'm running an IFD run with a metal-containing system. The metal moves during the calculation. How can I force the metal to stay fixed?

Article ID: 288 - How do I prepare a cytochrome structure with an oxygen bound to the heme iron?

Article ID: 261 - When I try to save images with Maestro 9.0.211, they turn out black and white and distorted. How do I fix this?

Article ID: 243 - What is the best way to place a membrane for my GPCR model to use in Desmond?

Article ID: 202 - I used SiteMap to find the binding pocket in my structure and now I want to do docking. Is it possible to use the SiteMap definition of the binding site as input to Glide?

Article ID: 194 - I would like to mutate a CH2 to C=O in a ring via FEP, but I don't see this as an option in Desmond's 'Ring atom mutation by FEP panel'. Is this mutation possible?

Article ID: 1472 - What platforms is Schrödinger software supported on?

Article ID: 1469 - Which version of ChemDraw can I use with Canvas?

Article ID: 1468 - Is there a way for me to save a customized appearance (e.g., atom colors, etc.) of a molecule so that those settings can be re-applied or automatically applied when I re-open the project file?

Article ID: 1467 - How do I configure the middle mouse button on my Lenovo laptop to use it for Maestro operations?

Article ID: 1466 - I have multiple fingerprints that I would like to combine and then use in the Canvas interface? Is this possible?

Article ID: 1464 - I have fingerprints that are not associated with a structure. Can I use them with Canvas?

Article ID: 1463 - Is it possible to use a project generated with Suite 2011 in Suite 2010?

Article ID: 943 - How can I create a movie or animation from Maestro?

Article ID: 61 - I am running Prime Structure Prediction on a Windows platform. How can I install the third-party executables and databases?

Article ID: 26 - Before running a docking experiment, how can I determine the active site location if my experimental structure doesn't contain a co-crystallized ligand?

Article ID: 25 - What should I do if I want to run a docking experiment, but my experimentally determined target structure doesn't have a bound ligand?

Article ID: 1459 - If I need to kill a Desmond FEP or Replica Exchange job, how do I make sure that I get the results back?

Article ID: 1456 - Maestro crashes on my Windows XP machine, which has an Intel 4 Series chipset graphics card. What is the problem?

Article ID: 1453 - When running Maestro 9.2 on my Lenovo laptop, the CPK, Ball and Stick, and Tube representations are not displayed. Is there a fix to this problem?

Article ID: 1452 - I would like to add parameters in the Desmond configuration file. How can I do that?

Article ID: 1450 - Can I view the trajectory from a Desmond FEP calculation with VMD?

Article ID: 1449 - When assigning force field parameters with Viparr, I get an error like the following:

Error: Struct 2, Res <"A",1> (A) not matched by any force field template with formula C(10)H(12)N(5)O(6)P(1)

Why is this?

Article ID: 1448 - Can I calculate total binding free energies with the Total Free Energy by FEP panel in Desmond?

Article ID: 1447 - When I try to copy a structure from ISIS/Draw and paste it into Canvas, it doesn't work. Why is this?

Article ID: 1074 - When processing large data sets, KNIME seems to be running out of memory. What can I do?

Article ID: 1446 - My SiteMap job was unsuccessful. There was a line in the log file with the error "Unable to open site-list file". What happened?

Article ID: 1445 - I have a job that is stranded. What does that mean? How do I get rid of it?

Article ID: 1444 - How do I make use of fingerprint data generated by Interaction Fingerprints (SIFT) in Canvas, the cheminformatics tool?

Article ID: 1440 - How do I replace a loop in structure A with one from Structure B?

Article ID: 1438 - I click the Plot button in the Simulation Quality Analysis or Simulation Event Analysis panels, but nothing happens. The analysis jobs ran fine, so why am I not able to plot the results?

Article ID: 1426 - How do I align independent chains in two or more protein structures?

Article ID: 1416 - How can I evaluate the volume of a cavity from SiteMap data?

Article ID: 1409 - Why am I having difficulty specifying a QSite QM region using backbone cuts?

Article ID: 1408 - How do I include a ligand in the QSite QM region if it is bound to a protein?

Article ID: 1407 - How do I include a metal ion in a QSite calculation?

Article ID: 1406 - How do I convert my QSite 4.0 input to the QSite 4.5 format?

Article ID: 1403 - Can QSite be run in parallel, (e.g., on a cluster)?

Article ID: 1397 - What is the QikProp CSV file and how is it organized?

Article ID: 1396 - Why does QikProp return non-integer hydrogen-bond counts?

Article ID: 1395 - Is there a limit to the size of structure QikProp can evaluate?

Article ID: 1394 - Do QikProp results vary for different conformers of the same molecule?

Article ID: 1393 - How is the QPlimits file used?

Article ID: 1392 - What happens if one of the QikProp input structures cannot be processed?

Article ID: 1390 - Can QikProp perform predictions on 2D structures?

Article ID: 1389 - What structure file types can QikProp read?

Article ID: 1388 - How quickly can I evaluate structures with QikProp?

Article ID: 1387 - What advantages does QikProp have over other Quantitative Structure-Activity Relationships (QSAR) and fragment-based property prediction methods?

Article ID: 1381 - When I try to run an Impref minimization from the Protein Preparation Wizard, I get a dialog box that says "Could not launch Impref minimization. Please check your installation.". How can I fix this problem?

Article ID: 1377 - Can I do a GPCR alignment on Windows?

Article ID: 1375 - I want to keep the job files from the Structure Prediction workflow, but they are deleted when the job finishes. How can I do this?

Article ID: 1374 - How do I apply crystallographic symmetry in a Prime refinement?

Article ID: 1372 - In the Prime Comparative Modeling workflow, Edit Alignment stage, the secondary structure prediction fails. What should I do?

Article ID: 1370 - My Prime refinement job finished successfully, but the log file states "Catastrophic Error in tn minimization". Do I need to worry about this message?

Article ID: 1369 - I successfully built a homology model with Prime, but my ligand does not have the correct bond orders. I want to use this structure as input for another Prime job (e.g., a loop prediction). What should I do?

Article ID: 1368 - My Prime refinement job died with an error referring to an 'xxxz' residue, where 'xxx' is a 3-letter residue name. What does this mean?

Article ID: 1364 - How do I run an extended loop prediction from the command line?

Article ID: 1363 - My protein structure contains a heme group (residue name HEM or HEC). How should I prepare the structure for Prime refinement?

Article ID: 1362 - Can in-house PDB structures be incorporated into the BLAST database for use with Prime?

Article ID: 1361 - Where can I obtain the GPCR-specific BLAST sequences needed to run with the Align GPCR option in the Edit Alignment step?

Article ID: 1358 - I installed Prime from the download site but there was no required or suggested third-party software included. What should I do?

Article ID: 1346 - I want to look at the job files from the Develop Pharmacophore Model workflow, but they are deleted when the job finishes. How can I do this?

Article ID: 1344 - Why doesn't Phase find any hypotheses when it looks like there is an obvious ligand alignment?

Article ID: 1343 - I marked a group as excluded in my feature definition, so why isn't the exclusion applied?

Article ID: 1342 - My Find Common Pharmacophores (phase_partition) job is taking too much memory. What can I do about it?

Article ID: 1341 - Should I generate ionization and tautomeric states when adding molecules to my Phase database?

Article ID: 1330 - I can't find menu items where they used to be in Maestro 9.0. Where are they now?

Article ID: 1131 - Can I run a Desmond job on Windows?

Article ID: 812 - Is there a way to export SiteMap surfaces to PyMOL?

Article ID: 1331 - Maestro has stopped working. I was able to run it before, but can't now. What can I do?

Article ID: 1329 - My flexible ligand alignment job fails. What can I do?

Article ID: 1328 - Why does surface creation run very slowly or fail?

Article ID: 1327 - When I undock a panel from the main window and open another panel, the undocked panel disappears. What can I do to fix this?

Article ID: 1326 - When I click the Reset View button on the toolbar, the workspace goes blank. What happened?

Article ID: 1325 - When I change the bond order or formal charge, the atoms are sometimes retyped incorrectly. What can I do?

Article ID: 1324 - Nothing happens when I click the Help button. What can I do?

Article ID: 1323 - I can't change the formal charge on an atom. What can I do?

Article ID: 1322 - How do I stop windows from migrating across the screen when I use Save Panel Layout and Restore Panel Layout?

Article ID: 1321 - Is there a limit on the size of structures that can be cleaned up with Clean Up Geometry?

Article ID: 1316 - On Windows, if I zip a project by right-clicking on it and sending it to a compressed (zipped) folder, the project cannot subsequently be opened in Maestro. What can I do?

Article ID: 1315 - Maestro isn't displayed properly on Windows when I use remote desktop to reconnect to a suspended session. What can I do?

Article ID: 1314 - When I assign a function key to a macro, it does something other than what I assigned it to. Why is this?

Article ID: 1313 - How do I prevent Maestro panels from being hidden behind other panels on my Linux machine?

Article ID: 1303 - Why does Maestro crash when importing a PDB file?

Article ID: 1301 - Keyboard shortcuts don't work. What can I do?

Article ID: 1300 - While opening a project, I get a message that cleanup is in progress. I know that this is not the case, so what can I do to open the project?

Article ID: 1299 - Maestro 8.0 runs, but panels such as the Workflow panels are failing to open. I notice that PYTHONHOME is empty in the startup message. How can I fix this problem?

Article ID: 1298 - Maestro fails on startup with an error that it can't load libXaw.so.7. What can I do?

Article ID: 1297 - What do I do if the colors in Maestro are being incorrectly displayed?

Article ID: 1295 - I want to run the Protein Preparation Wizard. What do I do?

Article ID: 1294 - How can I perform a series of tasks on a set of entries?

Article ID: 1293 - There are several tasks that I find myself repeating often. Is there any way in Maestro to automate these tasks?

Article ID: 1292 - How do I undo a series of Maestro actions?

Article ID: 1291 - How can I increase the tolerance for picking atoms in Maestro?

Article ID: 1290 - How do I rotate or translate only a portion of the structure in the Workspace?

Article ID: 1283 - Why is performance slower in normal mode than in stereo mode on my Linux machine?

Article ID: 1271 - How do I freeze the receptor in an Embrace calculation?

Article ID: 1270 - How do I set up Jumping Between Wells (JBW) or Free Energy Perturbation (FEP) computations with MacroModel?

Article ID: 1269 - When performing a conformational search, how do I judge whether the search has covered the complete conformation space?

Article ID: 1268 - I need to add parameters to MacroModel. How is this done?

Article ID: 1267 - How can I tell what force field parameters were used in a particular MacroModel simulation?

Article ID: 1264 - What structure file formats can be used with MacroModel?

Article ID: 1263 - When using GB/SA solvation in MacroModel, what value should be entered in the "Dielectric constant" field?

Article ID: 1262 - Can a Simulated Annealing procedure be performed with MacroModel?

Article ID: 1261 - Is it possible to restart a MacroModel dynamics simulation following a previous simulation?

Article ID: 1220 - What is KNIME?

Article ID: 1338 - Can I run Phase jobs on a grid?

Article ID: 1266 - MacroModel contains a variety of force fields. Which is best for my purpose?

Article ID: 1248 - How do I use LigPrep to prepare structures for QikProp?

Article ID: 1239 - What are the major differences between the three Liaison sampling methods—Minimization, Hybrid Monte Carlo, and Molecular Dynamics—in terms of calculated results? Which one should I use?

Article ID: 1238 - Can Liaison be run in parallel, (e.g., on a cluster)?

Article ID: 1219 - Can I use the energy analysis and NMR capabilities of NBO 5.0 with Jaguar?

Article ID: 1218 - Can I use the Babel keywords in Jaguar jobs on Windows?

Article ID: 1212 - Why don't I get any NBO output via Jaguar when I specifically request it?

Article ID: 1208 - Why are the gradients in a Jaguar optimization sometimes calculated numerically?

Article ID: 1056 - What should I do if my Jaguar job fails with the following error message (or something very similar):

"Record 24 of IO unit 81 (ionbyn) is empty"

Article ID: 966 - Can I run Schrödinger software as root?

Article ID: 1434 - I find there are too many items in the Maestro menus that I feel I will never use. Is there a way to edit the menus?

Article ID: 1433 - It's hard to see my ligand in Maestro because there are too many atoms from the protein in front, behind, and around the ligand. How do I clean up the view so it's easier to see my ligand?

Article ID: 1204 - Why do old versions of Jaguar fail to launch under recent Linux versions?

Article ID: 1203 - What types of files can Jaguar read and write?

Article ID: 1188 - Why does IFD fail in the initial Glide docking stage?

Article ID: 1180 - OPLS appears to be the only available force field for Impact jobs. Are there other options?

Article ID: 1121 - Following a protocore docking run, which file contains the results?

Article ID: 1120 - How can I run core-hopping jobs from the command line?

Article ID: 596 - Can Glide be run in a parallel (MPI) environment?

Article ID: 1112 - What is the Kelley criterion in Canvas Hierarchical Clustering ?

Article ID: 997 - PrimeX stopped in the middle of refinement with the error message, "number of iso-/aniso-tropic atoms does not match input". What does this error mean and what can be done to solve the problem?

Article ID: 54 - Can I perform a Jaguar geometry optimization and also have some atoms denoted as counterpoise (ghost atoms)?

Article ID: 49 - I am using the Python API to read in large structures but it seems there are errors. Is there a limit on the size of a structure that can be read using the Python API?

Article ID: 48 - Is there any way to run a different version of MOPAC through the Maestro GUI?

Article ID: 42 - When setting up a QSite calculation in Maestro there are fields for the charge and multiplicity. Which parts of the structure do these properties refer to?

Article ID: 753 - How do I select the top leads from a given pose viewer file and create a new pose viewer file, to which I append all the best leads from my Glide runs? I want to incorporate the table of values so I don't lose the scoring.

Article ID: 1099 - Prime gives a warning that the query sequence is invalid and must be fixed before continuing in the homology modeling workflow:

"Warning: the sequence is invalid at position 1: you must fix this before you continue"

What does this mean?

Article ID: 1095 - The ionizer doesn’t seem to recognize some kinds of structures, especially some fused rings. What can I do about it?

Article ID: 1094 - How do I kill a LigPrep job without having the output copied back?

Article ID: 1093 - When running LigPrep, is the bmin stage required?

Article ID: 1092 - What does LigPrep do by default when processing structures?

Article ID: 1077 - What are the major differences between the three Liaison sampling methods, Minimization, Hybrid Monte Carlo, and Molecular Dynamics, in terms of calculated results? Which one should I use?

Article ID: 1076 - How do I run simulations with multiple receptors in Liaison?

Article ID: 39 - Can LMP2 jobs be run in parallel ?

Article ID: 1086 - Are there shortcuts for common tasks in KNIME?

Article ID: 1080 - Can I run parallel jobs using the Jaguar Batch facility?

Article ID: 1069 - In KNIME, can the number of decimals or significant figures be adjusted for reporting, for example with the CSV writer?

Article ID: 1068 - What are KNIME labs?

Article ID: 1060 - Why aren't the results of a job I submitted to a batch queue incorporated into the Maestro project?

Article ID: 1053 - Are there any special requirements to run Jaguar in parallel via a batch queue?

Article ID: 1052 - What does it mean if the docking stage of an IFD run fails with an error about atom overlaps in the structure file?

Article ID: 1051 - What can I do if the Prime step in my Induced Fit Docking run fails?

Article ID: 1046 - How can I fix my protein structure in preparation for Induced Fit Docking?

Article ID: 1045 - How should I decide how many Prime CPUs and how many Glide CPUs to use for an Induced Fit Docking calculation?

Article ID: 359 - The Protein Preparation Wizard warns me that there are residues with missing atoms and that I should add the side-chains using Prime. I do not have Prime installed. What should I do?

Article ID: 1037 - What does a score of 10,000 for a ligand mean, and what can I do with these ligands?

Article ID: 1025 - What does the pose number correspond to?

Article ID: 1024 - Can I create a pose viewer file manually, by concatenating Maestro files?

Article ID: 1023 - Can I use poses generated with Glide SP or HTVS as input to XP docking?

Article ID: 1021 - How does Glide treat amide bond rotations?

Article ID: 581 - I used Glide XP to evaluate a crystal structure drug binding orientation. Why are the results reporting only one pose?

Article ID: 226 - I have trouble starting Maestro on my machine.

Locking assertion failure. Backtrace:
maestro: xcb_xlib.c:73: xcb_xlib_lock: Assertion `!c->xlib.lock' failed.

What does this error indicate?

Article ID: 23 - I have problems when I try to visualize plots in Canvas. The calculation seems to finish but the points are missing on the plot. What might be the problem?

Article ID: 1026 - What is the jobname_raw.mae file produced during a Glide docking job?

Article ID: 1022 - Can I use Glide XP for metal-containing systems?

Article ID: 1019 - How can I account for binding site flexibility?

Article ID: 1018 - Why are there three methods of specifying the Glide enclosing box center?

Article ID: 1017 - When setting up grids in Glide, what does the purple box enclosing a portion of my structure represent?

Article ID: 1016 - How do I prepare PDB files from the RCSB database for use with Glide?

Article ID: 1015 - What are the units of Emodel and GlideScore?

Article ID: 1012 - How long does it take to screen 10,000 compounds with Glide?

Article ID: 1011 - Can Glide dock ligands to RNA or DNA targets?

Article ID: 1007 - Can I view a Desmond trajectory while a simulation is still running?

Article ID: 1002 - I am setting up an Impact simulation with a continuum solvent model. To what does the Dielectric constant value in the Potential folder refer?

Article ID: 1001 - How do I copy a value for a property to other rows in the Project Table?

Article ID: 999 - How can I use the Protein Preparation Wizard to generate ionization and tautomeric states if I don't have an Epik license?

Article ID: 998 - What's the difference between the pK_a values produced by Epik in query mode and in scan (sequential) mode?

Article ID: 996 - I cannot get Desmond jobs to run under the SGE queueing system. What can I do?

Article ID: 995 - How can I efficiently set up the scheduling of Desmond jobs on an SGE queueing system?

Article ID: 992 - How do I generate variations with Epik while keeping the input form?

Article ID: 991 - How do I produce structures that are probable at pH 7 with Epik?

Article ID: 990 - How do I estimate the pK_a values for a set of structures?

Article ID: 987 - Can I use the Torque queuing system to run Desmond jobs?

Article ID: 985 - Where can I get a collection of side chains to use with CombiGlide?

Article ID: 983 - What parts of CombiGlide run in parallel or distributed mode?

Article ID: 982 - What should I do if I get an error message from Canvas about cumulative memory usage exceeding the limit?

Article ID: 981 - What are Canvas custom views, and how can I use them?

Article ID: 975 - Jobs that I am running from a Windows host are failing. Why might this be happening?

Article ID: 973 - Windows installation fails with the message:

The system administrator has set policies to prevent this installation

What can I do?

Article ID: 969 - My jobs fail and I see "Host key verification failed" errors. What does this mean?

Article ID: 968 - My job fails with the message


ImportError: No module named _md5

What can I do?

Article ID: 967 - I get the following error message when trying to run jobs:


/usr/bin/ssh: $SCHRODINGER/mmshare-vXXXXX/lib/Linux-x86/libgssapi_krb5.so.2 : 
no version information available (required by /usr/bin/ssh)

What do I do?

Article ID: 962 - Long jobs submitted to an SGE queue sometimes fail. What can I do?

Article ID: 961 - I've downloaded your products but I only have documents, not executables, in the tar file for the product. Why is this?

Article ID: 958 - How can I create additional ring conformation templates?

Article ID: 937 - Can I set up the ligand features for constraints in the Glide input file?

Article ID: 935 - Is there a way of finding out which of a set of compounds has the core in the same position as the core of my reference compound?

Article ID: 932 - When I ran XP Glide, I got three scores: docking score, XP GScore, and glide gscore. They were all the same. When are these scores different?

Article ID: 931 - Are the _grid.maegz and _rec.mae files written out by the Glide panel and IFD panel the same as the original input file for the receptor or do they contain additional information?

Article ID: 930 - The following message was displayed during Glide grid generation with flexible hydroxyls:

%IMPACT-I: Because of conflicts with input positions, number of movable atoms reduced from 3 to 2

What does it indicate?

Article ID: 926 - Can I dock RNA aptamers to a target with Glide?

Article ID: 925 - I'm interested in docking small molecules to RNA aptamers. Can I do this with Glide?

Article ID: 924 - I've performed ensemble docking with a set of grids, and I would like to merge the results, keeping only the highest scoring pose for each structure. Is there a way to do this?

Article ID: 922 - Is there a way to display protein grid points for different properties and probes so that docked ligands can be visualized in the context of grids? This would help to identify complementarity between ligands and a protein.

Article ID: 921 - My Glide docking run failed with a "confgen failed" error message. Why might this happen?

Article ID: 919 - I seem to have run out of tokens for running Glide, but I only have three Glide jobs running. How can this happen?

Article ID: 917 - I am modeling NADH in a protein complex, and I find that a nicotinamide ring is in a boat configuration with OPLS_2001 but is planar with OPLS_2005. Why the difference, and which is correct?

Article ID: 916 - Have liquids such as chloroform and DMSO have been validated with OPLS_2005?

Article ID: 914 - I want to modify the OPLS force field for Glide. Is there a way to specify the force field path that Glide uses?

Article ID: 911 - When trying to use the Maestro ActiveX control, I receive a "side-by-side configuration" error like the one below. Can I do something to address this issue?

System error. The application has failed to start because its side-by-side configuration is incorrect. Please see the application event log or use the command-line sxstrace.exe tool for more detail.

Article ID: 910 - Is there a specific equilibration protocol for membrane proteins in Desmond?

Article ID: 907 - Is it possible to run an MD simulation with implicit solvent using Desmond?

Article ID: 906 - Which membrane types does Desmond currently provide for use in membrane protein simulation?

Article ID: 905 - How many CPUs should I use for searching a Phase database?

Article ID: 901 - When I open a file browser to find some files, it doesn't list any files. What is wrong?

Article ID: 898 - I am having trouble getting a valid RMSD from the Superposition panel, because it seems that the atom numbering in my structures is different. Is there a way to have the superposition done and correctly identify the atom pairs independent of their atom numbers?

Article ID: 896 - Can I transfer my licenses from Linux to Windows?

Article ID: 894 - When using the Superposition panel to superimpose structures by ASL, what happens if one of the atoms is not in the ASL expression?

Article ID: 893 - I've added atoms to a protein, and the atom numbers are now out of order. How do I renumber them?

Article ID: 889 - Is there a way of making a random selection of compounds from my database from the command line? Can it be done by specifying the number of compounds rather than the percentage?

Article ID: 886 - I want to examine the atoms within 5 angstroms of a selected residue in a Desmond trajectory, and exclude other atoms from the display. Is there a way of doing this?

Article ID: 883 - I recently regenerated the Glide grid for a target, using a different ligand length. With the new grid, my old docking pose was not found. Why is this?

Article ID: 881 - How are the partial charges assigned to metal complexes for the impref minimization stage of protein preparation?

Article ID: 880 - When I build a model of a DNA/protein complex with Prime, the model has collisions between the protein side chains and the DNA. How do I fix this?

Article ID: 879 - Can I display DNA as ribbons in Maestro?

Article ID: 878 - Can I set up a Jaguar calculation from Maestro and run it on multiple structures in the same job?

Article ID: 877 - I would like to add a ligand to the active site of my structure and then refine the loop around it or optimize only the side chains. Can I do this in Prime?

Article ID: 869 - My protein molecule is bigger than the clipping planes and I can't see the full molecule. I also have a ligand in the Workspace, and the clipping is adjusted to it. How I can change the clipping if I have several molecules in the Workspace?

Article ID: 868 - When I start Maestro on Windows, I get an error message "failed to create scratch project in location", and I can't work in Maestro. How can I fix this?

Article ID: 864 - How do I start IFD in the Prime stage with Glide results from a separate Glide docking job? I want to access additional functionality (e.g., metal/hydrophobic/positional constraints) or modify Glide parameters that aren't configurable through the IFD interface.

Article ID: 863 - I need to renumber the atoms in the binding sites of several proteins, so that I can cluster and align them. Is there a way of doing this?

Article ID: 858 - I'm getting structures from MacroModel that seem to be incorrect, such as nonplanar carbonyls. I have restraints, but they are fairly weak. Is there anything I can do to fix this problem?

Article ID: 857 - Can I run multiple perturbations in a single Desmond FEP job?

Article ID: 854 - How long does Epik take to adjust the protonation state of a molecule?

Article ID: 851 - My Windows installation failed with this error message:

The system cannot open the device or file specified Internal Error 2755. 110, path-to-MSI-file

What is the problem?

Article ID: 848 - I was running a parallel (MPI) job, and it failed with a broken pipe error. Any idea why it failed?

Article ID: 847 - The Beep when picking preference doesn't seem to work on my Linux machine. Any idea why?

Article ID: 846 - When I try to use the Commands text box to change directories on Windows, the command fails. What is the problem?

Article ID: 840 - If I double-click a Sybyl .mol file on Windows, it doesn't get imported into Maestro. Why is this?

Article ID: 839 - The Choose User Profile dialog box is displayed when I open a help topic in Maestro. Is there a way to prevent this?

Article ID: 835 - I see the following warning when trying to open a Maestro project:

'' is an invalid current directory path. UNC paths are not supported.
Defaulting to Windows directory.

Is this a problem?

Article ID: 831 - I can't search the Maestro help on my Ubuntu machine. What can I do?

Article ID: 830 - I'm having problems searching the online help with Internet Explorer 7.0.5. Is there a fix for this problem?

Article ID: 829 - Adobe Reader crashes when I try to search the manuals on Windows. Is there a fix for this problem?

Article ID: 827 - When I run IRC calculations with Jaguar, I sometimes get no points, and sometimes points that don't make sense. What's the problem?

Article ID: 823 - How can I move a group in the Project Table?

Article ID: 820 - Do I have to center my MD trajectory before I can visualize it?

Article ID: 819 - What is the difference between "Combinatorial Screening", "Combinatorial Library Enumeration" and "Interactive Enumeration and Docking" in CombiGlide?

Article ID: 818 - How can I display more decimals for atom labels? For example, I would like to display the Jaguar Fukui indices "f-NN-LUMO" to 6 decimals instead of the default of 2 decimals.

Article ID: 817 - Why do I have to define some constraints in Glide during Grid generation and others during docking?

Article ID: 807 - How can I find representatives from a set of outputs from a Prime loop calculation?

Article ID: 806 - How are the XP descriptors useful in analyzing docking results?

Article ID: 804 - Does PrimeX do individual anisotropic B-factor refinement?

Article ID: 802 - When defining positional constraints in Glide, how do I tell which is atom number 1, atom number 2, and so on?

Article ID: 800 - How does Glide divide a ligand database file?

Article ID: 799 - Running the grid generation for Glide on Windows produces this error:

ImportError: DLL load failed: The specified procedure could not be found.

How do I fix this?

Article ID: 798 - What penalty terms are used in Glide XP that are not in Glide SP?

Article ID: 795 - I have a database divided into 22 gzipped Maestro files and would like to dock it with Glide using all the licenses we have. How do I do this?

Article ID: 794 - Can you tell me about the 'sa' and 'ln' ligand efficiency metrics?

Article ID: 792 - Does docking a set of ligands on two different platforms produce differences in the results?

Article ID: 791 - I find that glide_sort can't handle properties with multi-line values. The scores are getting shifted and glide_sort is filtering based on the wrong values, causing the rejection of all the poses. Is there a fix for this?

Article ID: 790 - Is there a document that explains any differences between the results from the different versions of Glide?

Article ID: 789 - My Glide XP refinement jobs are failing with memory allocation errors. The server has at least 40GB memory, and flexible docking jobs run fine. What could be the problem?

Article ID: 787 - Can you give some more information about the GlideScore terms, and how they have changed?

Article ID: 783 - My Glide docking run produced the following warning:

%IMPACT-W (warning): At line 57
%IMPACT-W: Confgen failed. Will skip this ligand.
SKIP LIG 54 (GTP): PROBLEM IN CONFGEN

What does this warning indicate?

Article ID: 781 - Can an inactive compound be docked? If so, what range of binding energies can I expect to see for inactives?

Article ID: 780 - Why are there ugly contacts in the Glide results?

Article ID: 779 - Is there a way to merge two .xpdes files?

Article ID: 768 - If I want to get 10-20 diverse conformations for Glide, how do I set the parameters for MacroModel CSearch or ConfGen?

Article ID: 761 - How can I add more than two dimensions into a Maestro plot?

Article ID: 758 - Is there a way of using QM-generated partial charges when docking ligands with Glide?

Article ID: 757 - Is there a term in the Glide score that rewards an aromatic C-H/acceptor interaction (where the aromatic C-H is acting as an H-bond donor)?

Article ID: 751 - How can I create a SMARTS pattern to use for a positional constraint in Glide?

Article ID: 744 - I'm using all my tokens, but want to run another job. Can I pause a running job and use the tokens to run something else for a few hours before resuming the job?

Article ID: 736 - If I run XGlide with PDB files containing ligands, will the Protein Preparation Wizard remove those before SiteMap?

Article ID: 734 - What does this message indicate?

%IMPACT-W: SKIPPING LIGAND: no metals in active site, structure generated by Epik requires metal binding.
SKIP LIG 773 (ASN 04109160): INVALID ATOM(S), ETC.

Article ID: 731 - Which part of the Glide output has the protein-ligand steric contact information, in the total score?

Article ID: 728 - I submitted a screening job, and later I closed Maestro by mistake without finishing the job, but the screening job seems to be still running. How is that possible?

Article ID: 721 - Is the term for pi-cation interactions included in docking as well as scoring?

Article ID: 719 - Is there a utility to convert old (format) DICE input files to the newer Glide keyword-value input files?

Article ID: 716 - I got the following error message in the Glide log file:

Impact: WARNING read_sd_data: Encountered multiple blank lines after a data field in input file, ignoring.

What does it indicate?

Article ID: 712 - I find that an XP Refinement job flips one of my urea-compound C-N dihedral angles 180 degrees. Is that a reasonable result?

Article ID: 697 - Do 'posenum' and 'confnum' indicate ranking?

Article ID: 696 - Is it possible to determine how the native pose would rank compared to the poses Glide actually produces?

Article ID: 690 - Does the internal energy term include any desolvation parameters? Where could I find out the contribution of solvation to the docking score?

Article ID: 689 - I would like to perform docking by placing the centroid of the first ring in the centroid of the native ligand. Is it possible to do so with Glide?

Article ID: 683 - For charged ligands, is there any distinction between SP and XP?

Article ID: 680 - It seems that Glide's conformation generator is not always preserving chirality when generating ring conformations. Is there a remedy for this?

Article ID: 676 - Can a sdf file containing tautomers, ionization states and ring conformations for a large number of compounds be docked using Glide, without any pre-preparation with LigPrep?

Article ID: 670 - How do I freeze amide bonds at their input conformations for peptides?

Article ID: 666 - I seem to be getting a lot of errors, and more than half of my molecules aren't docked. What could be wrong?

Article ID: 663 - I want to dock a peptide for which the position of one residue is known from the X-ray structure. Is there a way that I can keep this residue fixed and dock the rest?

Article ID: 661 - When I select 'Calculate rmsd to input sructure' in the Glide Ligand Docking panel, does this do the calculation based on all atoms or just heavy atoms, and does it superimpose the structures to find the best fit or do it 'in place'?

Article ID: 660 - I would like to do ensemble docking for some proteins in which residues in the binding site adopt different dihedral angles. How do I do this?

Article ID: 651 - I am unable to dock my ligand using core constraints. I receive the error "Core centroid is beyond tolerance 1.0 of grid box". What is wrong?

Article ID: 647 - How is 'Eint' calculated? What role do the 'vdw', 'coul' and 'hbond' components play in this?

Article ID: 646 - In the two systems I have been working on, making the inner box smaller or larger improves docking results, the outer box remaining the same. How would this happen?

Article ID: 644 - When I run my Glide docking job, I don't get a pose viewer file _pv.mae, even though I selected the option to write a pose viewer file. What has gone wrong?

Article ID: 639 - What is considered a good GlideScore?

Article ID: 635 - How do I interpret the values of the per-residue H-bond score?

Article ID: 634 - Is the effective charge displayed in the Glide log file the metal ion charge?

Article ID: 632 - Can one set ligand-atom positional constraints in IFD?

Article ID: 630 - The ConfGen Advanced mode with solvation gave no cis conformers for my molecule, but the Standard mode of Confgen finds at least one cis conformer. Why is this?

Article ID: 627 - How well does ConfGen perform on steroid-like molecules? Should I use MacroModel instead?

Article ID: 624 - I launched a calculation using ConfGen and found this error in the log file:

WARNING : MMCT ERROR(-4): mmct_atom_get_bond_atom(): 49 is an invalid bond index for atom 241 in CT 1274. Max is 16
FATAL mmconf_cgen_copy_params(): the ct has too many atoms: 435 limit is 200.
FATAL mmconf_cgen_ct_and_params(): problem with mmconf_cgen_copy_params.

How can I resolve this?

Article ID: 620 - In the ConfGen output, one of the properties columns was titled Times Found-OPLS2005. Could you let me know how theses values are computed and what they represent?

Article ID: 618 - QikProp has a feature to mark property values that are outside of the value ranges for 95% of known drugs. Is this list of known drugs available?

Article ID: 614 - We have access to infiniband and ethernet communication on a supercomputing system. Could you suggest which mode of communiciation would be preferable for running Glide jobs?

Article ID: 607 - How do I access the articles and papers listed on the publications pages of the Schrodinger website?

Article ID: 604 - Can you provide some details on how the strain energy is used?

Article ID: 598 - Is there a way to generate grids for a large number of pdbs? Also, is there a way to extract the ligand easily, so that it does not become part of the grid?

Article ID: 597 - Can an estimate be made as to how many compounds from the Glide screening results should be purchased, in order to come away with some "guaranteed" leads?

Article ID: 593 - When the .xpdes file is generated, I would like to export the terms to a .csv file via the command line. Is there a script for this?

Article ID: 587 - Glide was not mentioned in the modules listed in the machine info. How do I ensure we have Glide?

Article ID: 583 - Can I use Glide to dock molecules with more than 300 atoms?

Article ID: 571 - How are Emodel and the docking score used in ranking ligands?

Article ID: 566 - I would like to select the top 10 poses from Glide sorted by some specific property. Is there a command line tool for this?

Article ID: 565 - Can I dock metal ions with Glide?

Article ID: 562 - What is the difference between Strain Rescore (in the Script Center) and Emodel?

Article ID: 561 - Is there way to automate the process of docking to a set of receptor conformations, which includes grid generation for each of them?

Article ID: 559 - How do I stop a multi-processor docking job so that I can use the RESTART mechanism at a point in the future?

Article ID: 545 - Where did the OPLS_2005 metal ion parameters came from? Metals aren't discussed in the Jorgensen JACS 1996 paper. Were they added later?

Article ID: 543 - Are the OPLS-AA parameters for sugars, given in J. Comput. Chem. 23 (2002) 1416-1429, implemented in Schrodinger force fields?

Article ID: 542 - I am working on a protein that contains a heme. Has there been any development work on parameter sets for heme compatible with OPLS_2005 or OPLS_2001?

Article ID: 537 - When attaching a script to the ePlayer buttons, the Workspace does not actually update to reflect the script operations until I manually move the cursor over the Workspace window. If I simply keep clicking on the ePlayer buttons to step one at a time through structures without moving the mouse over the workspace, the changes made by the script never show up in the Workspace. Why does this happen?

Article ID: 534 - When I do a flexible ligand alignment with multiple ligands selected and included, the Workspace is not updated with the aligned structures. It works when ligands are only selected. Is there a fix for this?

Article ID: 504 - In the Prime GUI, I need to be able to see 3d selections reflected in the sequence, and sequence selections reflected in the 3d structure. Is there any way to do so?

Article ID: 498 - Is there a command-line tool to delete unnecessary columns from a big project?

Article ID: 496 - I find that on Windows, the Import button in the Protein Preparation Wizard fails to retrieve the pdb from local pdb database. What would cause that?

Article ID: 492 - In the 2D viewer, I want H-atoms only on the heteroatoms, but not on the carbons. Is there any way to do this?

Article ID: 489 - On the output of the following commands:

glxinfo | grep -i opengl -m 3 and
glxinfo | grep -i direct

I got this:

NVIDIA: could not open the device file /dev/nvidiactl (Permission denied).
NVIDIA: Direct rendering failed; attempting indirect rendering.

What does it indicate?

Article ID: 483 - I tried to import a pdb file but I got this error:

Total models (-num_models) was incorrect.

What do I do?

Article ID: 476 - Is there a way to superimpose molecules onto a ribose backbone reliably?

Article ID: 475 - I use multiple Maestro sessions on different desktops on my Linux workstation and when the help is open in a different session, I have to find it and close it in order to start a new one. Is there a way to open multiple help sessions from Maestro?

Article ID: 471 - Is it possible to have a workstation on Windows 2008 and use Reflection X to log into a Linux system and launch Maestro?

Article ID: 457 - I use a SUSE enterprise desktop Linux 11. Would the license continue to work if I install RedHat enterprise 5?

Article ID: 448 - I would like to run a superposition from the command line and not from the graphical interface. Is there any way to script such an operation?

Article ID: 445 - How do I rename an entry group?

Article ID: 443 - I'm using the Workspace Selection tool to generate a SMARTS pattern. How do I copy the SMARTS into a text file?

Article ID: 435 - How can I correct some AMBER-generated PDB files and make them format-compliant and readable by Maestro?

Article ID: 427 - When trying to read proteins I get warning messages such as :

WARNING check_residue: no template for residue 500 (INH ), chain 'B'.

What does this mean?

Article ID: 404 - How do I get rid of all the No Flip and Flip labels on the protein after protein preparation?

Article ID: 403 - Is there a script I could use that reports the results of structural alignment? Using the Atom Selection interface I can readily identify the residue number, but is there a command to do this, so I can write a script that outputs the corresponding residue numbers?

Article ID: 400 - What is the best way of clustering 200 compounds based on similarity?

Article ID: 368 - The "check for updates" feature seems to run constantly and when Maestro is open, causes it to freeze. What do I do?

Article ID: 352 - My Desmond job fails with:

r_clone requires too large of a clone buffer. Use fewer nodes or a smaller r_clone

What can I do?

Article ID: 349 - In Phase, how do I modify the way rings are defined? I want the rings to be perceived as hydrophobes.

Article ID: 342 - How do you center on an atom in the Workspace?

Article ID: 331 - I notice that, during ligand preparation with LigPrep, some compounds are eliminated in the final optimization stage. Why is this?

Article ID: 318 - Can I run counterpoise calculations with QSite?

Article ID: 315 - The Electrostatic Potential (ESP) is an integral over the wave function (which for QSite includes effects from the MM point charges) plus a sum over nuclei. For QSite, does this latter sum also include the MM point charges?

Article ID: 314 - What are the units of the Electrostatic Potential (ESP) computed by Jaguar or QSite?

Article ID: 313 - In what version of Glide did the SP GlideScore start to include the special XP rewards (e.g., hydrophobic enclosure, correlated H-bonds)?

Article ID: 312 - What was the first Gilde version that included post-docking minimization and used it as the default?

Article ID: 311 - I could not start Maestro because of a license problem. Looking at the 'lmgrd*.log' file, there are errors regarding the vendor daemon

10:12:08 (lmgrd) SCHROD using TCP-port 35831
10:12:08 (SCHROD) Failed to open socket to lmgrd, Exiting
10:12:08 (SCHROD) EXITING DUE TO SIGNAL 37
10:12:08 (lmgrd) SCHROD exited with status 37
(Communications error)

How can this be fixed?

Article ID: 303 - How can I constrain metal ions while running MD?

Article ID: 300 - How can I use the General Amber Force Field (GAFF) in Desmond?

Article ID: 298 - How can I view a Desmond trajectory in VMD?

Article ID: 295 - I want to run the bennett.py script manually to perform analysis on a subset of frames. How can I do that?

Article ID: 294 - Some of my Prime jobs die during IFD. How does it affect my results?

Article ID: 290 - What is the NUSECONS keyword in the Glide docking jobname.in file? How does it influence the constraint settings stored in the jobname.feat file?

Article ID: 287 - How do I deal with the following error when launching Maestro on 64-bit Fedora Linux?

QGLContext::makeCurrent(): Cannot make invalid context current.
WARNING This display cannot support the graphics settings needed by
WARNING Maestro. Please try a different graphics card or see if
WARNING your graphics card can be reconfigured Maestro: Error initializing Maestro
Maestro: ** abnormal termination **

Article ID: 271 - Can I import a Maestro file as a homolog in the Prime structure prediction workflow?

Article ID: 266 - Can I generate Glide grids with hydrophobic constraints from the command line, or via a Python script?

Article ID: 259 - If a VSW job includes Glide Grid Generation with a metal constraint, why does it fail with an error like "Runtime Error: glide.py: constraint 'metal1' is not defined for the grid"?

Article ID: 258 - Can a 'Develop pharmacophore' project generated on the command line be converted to a Maestro project?

Article ID: 255 - Is there a way to keep the vectors for acceptors/donors/aromatic rings when generating hypotheses using the free-style tool?

Article ID: 252 - Is it possible to run a Phase 'Find matches' job on an SD file from the command line, using multiple processors?

Article ID: 249 - Does Glide scale well on multiple cores/cpus? Are there any particular recommendations for running parallel Glide jobs?

Article ID: 240 - Why is there a discrepancy between the vdW energies from oplsaa.vdw and the .mmo file?

Article ID: 235 - My cluster uses a Myrinet network. Can Desmond use this?

Article ID: 220 - When I run the Generate PhaseDB GUI, I notice that the ConfSites stage runs on only 1 processor even though I allocate multiple processors and subjobs. I have 2500 ligands. How can I get the ConfSites stage to use multiple processors?

Article ID: 219 - Can I generate new GB/SA solvation parameters for MacroModel? Is there a solvation model for DMSO?

Article ID: 218 - I colored my Canvas data column by the color scheme "Color Wheel". What do the colors mean ?

Article ID: 217 - Can my Canvas computations be set to automatically incorporate into the Canvas project ?

Article ID: 211 - What cluster radius should I choose in Leader-Follower clustering ?

Article ID: 209 - When using Canvas Diversity Analysis, how big of a subset can I select, and how do I choose the value of the exclusion sphere size ?

Article ID: 207 - When I perform a docking job that uses flexible hydroxyl groups on the receptor, what receptor conformational states are used, and how much longer will it take my calculation to run? How can I set up such a calculation?

Article ID: 205 - I got very bad results on a pKa calculation with Jaguar. What did I do wrong in my setup?

Article ID: 204 - How long does it take to create a Phase database?

Article ID: 203 - How long does it take to screen a Phase database?

Article ID: 196 - I run QikProp on my molecular input, but receive an odd error message, "Reactive FG: heteroatom in 3-ring", when there is no such functional group. What does this mean?

Article ID: 193 - My IFD jobs are failing at random points after running for a while. I get an error message like this in the main .log file:

filehandle = open( IFD_Stage.jobRestartFile, "w" )
IOError: [Errno 5] Input/output error: 'jobs.restart'

What does this mean?

Article ID: 189 - Why is there a a partial charge cut-off for scaling the van der Waals radii in docking?

Article ID: 188 - Do I need to calculate charges and provide ligand force field parameters for simulation in Desmond?

Article ID: 187 - What ensemble should I use for my molecular dynamics simulation in Desmond?

Article ID: 185 - Does IFD change the backbone coordinates of my protein, or does it sample only side-chain orientations?

Article ID: 184 - My initial IFD calculation does not appear to produce the correct binding mode. What can I do to improve the results?

Article ID: 183 - Can I use Induced Fit Docking for virtual screening?

Article ID: 172 - How good is QikProp in real world usage?

Article ID: 158 - I have built my GPCR homology model but I want to create a disulfide bond in my extracellular loop region. Can I do this in Prime?

Article ID: 156 - The "align GPCR" mode in Prime gives me a poor alignment for helix 5 in my class A GPCR. Why is this?

Article ID: 155 - I have a class B or C GPCR sequence, can I use the "align GPCR" mode to align my sequence to the template?

Article ID: 145 - Do I need to generate multiple conformations of my ligands to run Glide?

Article ID: 139 - How can I import a FASTA file containing a multiple sequence alignment into the Prime GUI?

Article ID: 135 - After running Phase Shape I noticed that two columns are returned: "Shape Sim" and "Shape Sim Pure". Could you explain the difference and when and why to use one or the other?

Article ID: 134 - I'm trying to run a Phase Find Matches job using multiple processors but the -minRec 100 keeps resetting the number of processors for running the job to 1. I generated multiple phasedb subsets for the job but minRec still resets the processors to 1. Why is that? I would like to use all of my available processors.

Article ID: 129 - Does Phase report the best or the first alignment in the Project Table, after screening a database with a hypothesis?

Article ID: 125 - Should excluded volumes be used in the Phase QSAR model building process?

Article ID: 124 - My job failed with this error message:

FATAL: No job directory

What do I do?

Article ID: 123 - Which is faster: shape screening or pharmacophore screening? And does having excluded volumes affect the search speed?

Article ID: 118 - Where can I find the Desmond absolute solvation FEP dataset that was used for the Shivakumar et al paper in JCTC in 2010?

Article ID: 115 - My QSite calculations are running for a long time and are not converging. What can I do?

Article ID: 114 - The energy obtained with Jaguar is very different from results obtained with other QM software using the same basis set and the same functional. Why is this?

Article ID: 112 - How do I assess the quality of my protein structure?

Article ID: 106 - Is it possible to view trajectories from a replica exchange simulation?

Article ID: 104 - I would like to estimate the free energy over different time ranges of the production trajectory in an FEP simulation. Can I do that?

Article ID: 101 - QikProp reports the number of likeley metabolic reactions. What are these?

Article ID: 99 - Can I generate conformers with LigPrep ?

Article ID: 84 - How do I estimate the solvation energy of a small molecule using molecular mechanics ?

Article ID: 75 - I want to add internal restraints to my Desmond simulation. How can I do that?

Article ID: 71 - When using QSite can I make a cut inside a ligand rather than putting the whole ligand inside the QM region ?

Article ID: 64 - I'm running VSW with a small number of ligands. How can I get multiple poses per ligand for visual examination?

Article ID: 40 - I am running a Jaguar calculation on a structure with 8 atoms. Can I use for example 16 CPUs to make the calculation run faster ?

Article ID: 37 - How do I obtain more information on command line scripts, e.g. fragment_join.py?

Article ID: 20 - Can I use any implementation of MPI with Desmond?

Article ID: 19 - Can I restart the frequency part of a Jaguar job? This part of the calculation seems to take the most time.

Article ID: 17 - In a TDDFT Jaguar calculation how many roots can I calculate?

Article ID: 15 - Can I use the MMFF force field with Desmond?

Article ID: 12 - What is the maximum number of processors / cores that can be used in a Jaguar calculation?

Article ID: 11 - I just performed a DFT calculation using Jaguar and the HOMO was higher than the LUMO. How can this be?

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