Dear all,
I am running MD simulations which contain a small molecule with a sulfonamide group, which is substituted at the para position on a benzene ring. I have noticed that there is a conformational abnormality which I think is caused by an incorrect parameterisation with respect to the dihedral component. The dihedral angle between the two oxygen atoms in the disulfide group are approximately 180 degrees and 0 degrees, respectively. We would expect a dihedral angle close to 156 degrees and 23 degrees. I am using the general amber force field (GAFF), where the dihedral component for the atoms in question are defined as such:
"X -ca-sy-X 6 7.800 180.000 2.000 estimated, same as X-ca-s6-X"
Can anyone shed any light as to why I am getting such strange dihedral angles, or if there is an alternative Amber compatibile force field parameter that accounts for sulfonamide groups more accurately?
Regards
Serge
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Received on Mon Sep 07 2015 - 10:30:04 PDT
