Hi all,
I am trying to parameterize a ligand that contains a deprotonated phenol group.
The oxygen is not exactly double bonded, but the C-O bond distance is very short (1.24 based on QM optimizations). Using parmcal this distance places it between a double bond (1.23) and a conjugated bond (1.26).
I have been looking through the force field files for amber and gaff for a good atomtype for the oxygen, but I am not sure which one to use.
Does anyone have a good suggestion for one to use, or should I proceed to create one on my own?
In either case, would you suggest adding special bonded parameters for this bond, perhaps using values from parmcal?
Best regards,
Jesper
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Jesper Sørensen, Ph.D.
Postdoctoral Researcher, Amarolab
Department of Chemistry and Biochemistry
University of California, San Diego
9500 Gilman Drive
La Jolla, CA 92093-0340
http://amarolab.ucsd.edu
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Received on Fri Sep 14 2012 - 17:00:03 PDT
