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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


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


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

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