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

If the atom types are supported in the OPLS_2005 force field, you can dock them with Glide 5.7 or later (Suite 2011 on), which uses OPLS_2005 by default for both grid generation and ligand docking.

For earlier releases, some elements and atom types, such as boron, are not supported in the default force field used by Glide, OPLS_2001, so compounds containing them are skipped during docking. If they are supported in OPLS_2005, you can use OPLS_2005 to dock these ligands. Glide has not been optimized for OPLS_2005, but should perform well. To find out if OPLS_2005 supports all the atoms in your ligands, you can run an Impact energy calculation with the OPLS_2005 force field.

To run Glide jobs with OPLS_2005, you can set the environment variable SCHRODINGER_MMIM_GLIDE_FF to OPLS_2005 prior to starting your Maestro session. (Information on setting environment variables on Windows is given in the Installation Guide.) Alternatively, you can add the line:

FORCEFIELD  OPLS_2005

with a text editor to your input file, jobname.in, and then submit this job from command line with

$SCHRODINGER/glide jobname.in

If the elements or atom types are not supported in OPLS_2005, or you want to try modifying the OPLS_2001 force field (for example by supplying custom parameters or copying parameters from the OPLS_2005 parameter files) please contact Schrödinger Technical Support (help@schrodinger.com) for instructions.

Keywords: glide, atom types, boron, unsupported atom types, simplified input file, Maestro

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