Hello Serge,
I agree with you that your observation of the torsion angles are coming
from the parameter that you listed if you assigned the sulfur atom to be
sy, which I assume is an antechamber assignment. As far as I know, of the
available force fields, GAFF is your best chance at modeling this chemical
functionality.
However, the chemical group is small enough that would allow one to do
some quantum mechanics to check the gaff parameter, or to do your own
parameterization. If you have not done this before, I might be able to help
you. If you are interested, please contact me privately.
Bests regards,
Karl
On Mon, Sep 7, 2015 at 7:16 PM, Jovanovic, Srdan <
srdan.jovanovic.13.ucl.ac.uk> wrote:
> 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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>
--
Karl. N. Kirschner, Ph.D.
Research Associate
Bonn-Rhein-Sieg University of Applied Sciences
Grantham-Allee 20, 54757 Sankt Augustin, Germany
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Received on Tue Sep 08 2015 - 01:30:04 PDT
