From: Vermaas, Joshua (
Date: Fri Sep 02 2016 - 10:54:00 CDT

Hi Jrhau,

The pose SHOULD NOT MATTER when it comes to CGenFF, since CGenFF makes the atom type assignments based on connectivity. If the two poses give you different results, that is because CGenFF is interpreting them as two different molecules, since its heuristics sometimes identify bonds where there shouldn't be any. Check the mol2 files that came out of CGenFF as well. They *should* be identical, but if its giving you different penalties, for whatever reason they may not be, and you'll need to figure out which is actually correct.


On 09/02/2016 12:03 AM, jrhau lung wrote:
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