Article ID: 1470 - Last Modified: June 3, 2011
Sometimes the results returned from Glide have slightly distorted aromatic rings. Can I prevent this?
Distorted aromatic rings are not necessarily unphysical, because the out-of-plane bending mode frequencies are not infinite. There are some target-ligand combinations where interactions can outweigh the improper torsions in the OPLS force field, so the distorted rings are not a bug. However, nonplanarity can also be a result of rigid-receptor docking.
You can significantly increase the force constant for the out-of-plane bending of aromatic rings (and other groups that should be essentially planar) by selecting "Use enhanced planarity force field parameters" in the Settings tab of the Ligand Docking panel, or by adding the following line to the Glide input file (jobname
The increased force constant should prevent rings and other groups from distorting out of the plane. This term does not affect post-docking minimization, so you should probably turn off the post-docking minimization to keep the rings planar.
#244: Sometimes I find distorted phenol rings coming out of a Glide docking run. Why is that and how should I get rid of th...
#1036: Why are there nonplanar aromatic rings in docked poses?
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