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1521 results

How do I perform a hydrogen-only minimization of my molecule collection,...

February 16, 2015
This can be done using the MacroModel substructure facility. In Maestro, open the Minimization panel (Tasks → Minimization → Force Field), choose the structure source...

Is it possible to generate the mirror-image stereoisomer of a compound, by...

September 2, 2019
Yes, you can do this in Maestro. Select the compound in the workspace, right-click and select Additional Edits → Invert Chirality. You can also use the Maestro...

In the QikProp descriptors, what is the difference between QPLogS and CIQPLogS?

August 11, 2015
These are aqueous solubility predictions. The CI in CIQPLogS stands for "Conformation Independent". The CIQPlogS value has a different regression equation from QPlogS. If the...

Can I specify a release-independent licenses directory on Linux with the...

February 22, 2016
Starting with the 2015-4 release, our software supports the use of a release-independent licenses directory /opt/schrodinger/licenses in which licenses files with file extension ....

What is the small down-arrow on the Maestro tool bar buttons? When I click the...

August 31, 2018
The down-arrow indicates that a menu is available for the feature. You need to click and hold on the button to open the menu. You might need to hold for a full second or so. A...

I colored my Canvas data column by the color scheme "Color Wheel"....

December 4, 2010
This scheme is intented for integer-valued data. A selection of colors from the spectrum is applied to individual integer values. For real-valued properties, the value is rounded...

How can I take into account long-range interactions in polarizability and...

May 19, 2014
The best option is probably to use the M06-2X functional with the Rappoport-SVPD basis set. Note that although corrections like the D3 correction account for dispersion effects,...

Why does Covalent Docking quickly fail with an 'mmct_ct_extract_atoms...

October 9, 2015
A Monitor panel (i.e., log file) error like this: Error: mmct_ct_extract_atoms returned error code -4 (MMCT_ERROR) for arguments (34, Bitset(61)). See the mmerr log (stderr...

When running the hydrogen bond assignment stage of the Protein Preparation...

August 11, 2015
This is likely be due to a file permission problem, which occurs on Linux machines. To fix it, change the permissions on the file $HOME/.python-eggs, by entering the following...

What is the definition of the "clustering strain" property that is...

February 22, 2016
The script uses the hierarchical clustering feature of Canvas. The 'Clustering strain' is the ratio of the sum of adjacent pairs of distances in the dendrogram to the sum of the...

How do I generate a protein multimer structure from the monomer using the...

October 29, 2021
There are several options that you can use: Use the Protein Preparation Wizard Type the PDB ID in the text field. Select the "Biological unit" checkbox. Click on "Import"...

The Schrodinger KNIME extensions aren't working. What should I do?

May 13, 2020
You can use the Setup Diagnosis node to diagnose the problem.Start KNIME, if it is not already running.Add the Setup Diagnosis node to the workspace (under Schrödinger → Tools in...

I am getting an error on my Linux machine that includes: Syntax error: word...

November 5, 2014
This can happen if the LSB package is not installed. See Article 1437 for instructions on installing this package. It can also happen if you are running with a 32-bit Linux...

How can I calculate relative binding energies of protein-protein complexes?

April 16, 2015
This can be done using Prime MM-GBSA. A warning is displayed about the ligand having more than 300 atoms when you start the job from the GUI. However, this is just a warning, and...

Which GPU cards are supported for FEP or Desmond simulations?

November 4, 2019
We support a set of GPU cards, which we test daily and have found to be stable and reliable and to deliver good performance. See the Supported Platforms page for a list of the...

I am trying to view the Ligand Interaction Diagram of a ligand I have docked...

May 4, 2018
The Ligand Interaction Diagram uses Maestro's automatic ligand detection parameters (e.g., molecule size range, excluded residue types), which you can change via the Maestro...

How do I find the names of the properties in a structure file? I want to use...

February 19, 2015
You can use the proplister utility, which reports on the properties in one or more Maestro or SD files. To find all the names, use the -a and -l options. By default the internal...

How do I enable 3D stereo on Windows?

August 5, 2019
To use 3D hardware stereo on Windows for viewing structures in Maestro, you must have the necessary graphics card and driver. See Article 1745 for the hardware requirements. As...

I'm seeing spacing problems in the Project Table column headings. Is there...

April 20, 2015
Spacing problems in places such as table headings in the Project Table can be caused by the lack of a standard fixed-width font. You can set the fixed-width font by editing the...

How do I find a specific property in the Project Table?

March 13, 2014
Click the Tree button on the toolbar or choose Property → Tree on the menu bar. Search for the property in the search box and then right click on the property and choose...


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