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1553 resultsWhat is the definition of the "clustering strain" property that is...
February 22, 2016The 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...
February 10, 2015Here are two approaches that you can use:
Use the Biological Assembly from the RCSB web site.
On the rcsb.org web site, search for the PDB structure that you want to use...
The Schrodinger KNIME extensions aren't working. What should I do?
September 19, 2013You 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 Schrö...
Where do I get the Schrodinger free nodes, and is there extra setup up to do?
April 21, 2015The Schrödinger free nodes are available as a zipped update site here. To use most of them you need to set the SCHRODINGER environment variable to your Schrödinger...
I am getting an error on my Linux machine that includes: Syntax error: word...
November 5, 2014This 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, 2015This 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 12, 2015We only support a limited 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...
I can't launch any jobs from my Linux machine using the 2015-3 release and...
November 11, 2015If your Linux host name contains uppercase letters you may have run into a problem with host name resolution that is specific to Linux machines and the 2015-3 release.
The...
I just updated to the 2015-4 release, and the controls for selection of the...
February 22, 2016The ability to select individual GPUs was disabled in the 2015-4 release to avoid job failures under some circumstances, and will be completely removed in a future release. The...
Does Schrodinger software run on Mac OS X 10.9 (Mavericks)?
February 12, 2014Yes, from the 2014-1 release, Mac OS X 10.9 (Mavericks) is supported.
As Apple released Mac OS X 10.9 (Mavericks) in late October 2013, it was not possible to fully test the...
I am trying to view the Ligand Interaction Diagram of a ligand I have docked...
May 5, 2015The Ligand Interaction Diagram uses Maestro's automatic ligand detection parameters (e.g., molecule size range, excluded residue types), which you can change via Workspace →...
How do I find the names of the properties in a structure file? I want to use...
February 19, 2015You 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?
November 11, 2015To 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, 2015Spacing 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, 2014Click 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...
Is it possible to perform TDDFT calculations with QSite ?
March 13, 2014Yes, you can perform TDDFT calculations with QSite provided the QM region is defined by hydrogen caps or as a separate molecule.
Another program I use can no longer read Maestro files. Did the format change?...
February 17, 2014Starting with the 2013-1 release, Maestro files are written with less redundant information to save space and improve processing efficiency. In particular:
There is less white...
In Maestro on Windows, I used the Scripts menu to install scripts into the...
August 12, 2014This is likely a permissions problem. The common area is within the the Schrödinger installation directory in C:\Program Files, and requires administrator or power user...
When I perform an NBO calculation my job fails with errors of the form MEMALL:...
August 12, 2014There is a limit on the amount of memory that is available for NBO calculations. The best way forward might be to use a higher energy threshold (NRTTHR) to reduce the memory...
When docking ligands with large rings, I get an error saying "Ring larger...
February 26, 2015This error is due to is a limitation in Glide's conformation generator in releases prior to 2014-3. Glide checks for ligands that would fail in flexible docking due to the ring...