[AMBER] formal charge of the ligand

From: Mary Varughese <maryvj1985.gmail.com>
Date: Fri, 27 Jun 2014 15:05:55 +0530


In the MD study of target-ligand interaction, if the ligand are acidic
compounds like caffeic acid,
should i use a formal charge 0 (COOH) or -1 (COO-).
Is anyone familiar with MD simulation involving -ve charged ligands?
It would be very much helpful if any one could suggest.

Thanking you

Mary Varughese

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Received on Fri Jun 27 2014 - 03:00:03 PDT
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