Knowledge Base

Article ID: 659 - Last Modified:

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?

The OPLS_2001 force field for the ligands doesn't have explicit parameters for isonitriles or isocyanates, and as a result, it bends the C-N#C bond angle. OPLS_2005 treats these functional groups correctly. OPLS_2005 is the default force field for docking from Suite 2011 on.

For earlier suites, there are two possible workarounds.

First, you could continue to use OPLS_2001, but turn off post-docking minimization (on the Output tab). Only the post-docking minimization step of Glide does a full (as opposed to torsion-only) force field minimization, allowing bond lengths and bond angles to vary, so turning off this step will maintain the input bond geometries.

Second, you could run Glide with post-docking minimization, but use OPLS_2005 instead of OPLS_2001. To use OPLS_2005, add the line

FORCEFIELD OPLS_2005

to your jobname.in file, and then run the job from the command line

$SCHRODINGER/glide jobname.in

Keywords: isocyanate, isonitrile , collinear, OPLS_2001, OPLS_2005, Glide

Back to Search Results

Was this information helpful?

What can we do to improve this information?


To ask a question or get help, please submit a support ticket or email us at help@schrodinger.com.
Knowledge Base Search

Type the words or phrases on which you would like to search, or click here to view a list of all
Knowledge Base articles