Article ID: 659 - Last Modified: May 1, 2012
I have some problems docking a molecule that contains this fragment
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 jobname.in file, and then run the job from the command line
Keywords: isocyanate, isonitrile , collinear, OPLS_2001, OPLS_2005, Glide
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