From: jrhau lung (
Date: Fri Sep 02 2016 - 00:12:03 CDT

To simulate the binding affinity between the ligand and receptor, how
should I choose a lignad conformation to generate CgenFF.

My lignad in docking pose receive a higher CgenFF penalty score (between 50
to 100) than in native pose.

Should I just ignore the warning message in QwikMD or choose a CgenFF
parameter with a much lower penalty score generated from native pose?

Thanks for any suggestion