Yun,
> I have some sulfonium molecules with a chiral tetrahedral sulfur atom.
> Interestingly, the RESP charge calculated for this positive sulfur atom is
> only around 0.1.
You could:
- derive the RESP charge values for the entire molecule (selecting one
or two representative conformations; _single_ conformation, multiple
molecule charge fitting; conformations considered as different
molecules) and compare to what you got when splitting in two building
blocks.
- compare with ESP charges (equivalenced from the RESP output and not
equivalenced from the Gaussian output) & mulliken charges (not
equivalenced from the Gaussian output) for information; the statistics
module of R.E.D. Server/R.E.D. IV provides this feature... This is
always interesting to compare to other 'type' of charges the charge
values of a new chemical group...
> I also wonder how to set atom types for this sulfur from ff99SB.
I think you should define a new FF atom type for this S+.
- then, do you want to/can you define new vdW parameters?
- your S+ is in a cycle; I would develop several/new dihedral FF
parameters for key dihedrals around the S+ atom.
> Would the
> configuration flip if I am using ff99SB parameters for disulfide sulfur
> atom?
I never ran MD simulations on this type of asymmetric atom with only
three atom connectivities; People in the Amber mailing list should
have the experience of this type of problem...
Fore sure I would follow the chirality of this S+ center during MD &
geometry optimization when using your FF...
regards, Francois
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Received on Sat Jun 16 2012 - 00:00:03 PDT
