I'm seeing nonplanar aromatic groups in my protein when I minimize with Prime. Is there a way to fix this?

Both Glide and Prime support options to encourage aromatic rings to be more planar. From the Suite 2011 release of Glide on this option is in the Settings tab of the Glide docking panel, as "Enhance planarity of conjugated pi groups" (Suite 2012 on), or "Use enhanced planarity force field parameters" (Suite 2011).

If selected, the following keyword setting is written to the docking input file:

FORCEPLANAR YES

In Prime, you can add the following keyword to the input file:

PLANARITY_RESTRAINT

It can take values of low/normal/high or a numerical value. The low/medium/high keywords correspond to values of 1/5/10.

If you see nonplanar rings, you can try the above option and see if it improves the planarity of your system.

Please keep in mind, however, that according to high-level QM calculations, there is not much of an energy penalty for distorting aromatic rings by a few degrees.

Keywords: aromatic, nonplanar, planar, Glide Prime, distorted

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