On Thu, Jul 4, 2013 at 9:08 AM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Thu, Jul 04, 2013, Karl N. Kirschner wrote:
> >
> > Using the coordinates posted in your original email, one can see that
> > the H14 atom has the same x,y,z coordinate values as the O1 atom.
>
> This is a common problem with simple parameterization of phosphates,
> sulfonates and similar groups. If the H atom has zero LJ parameters, the
> angle parameters are not enough to keep the H away from a neighboring
> oxygen
> bound to the same P or S atom, and the electrostatic attraction will bring
> the
> two atoms to the same position.
>
> >
> > I am doing MD simulation with GAFF, but the sulfonic acid group became
> > a three-membered ring which includes two oxygen atom and one sulphur
> > atom.
>
> My guess above may be wrong, since GAFF hydrogens don't have zero LJ
> parameters. But it's worth a check.
I thought some did... Lines 5703 and 5706 of gaff.dat define ho and hw
with 0 for both epsilon and R. I don't think hw is used often (ever?), but
ho would be, unless I'm missing something?
All the best,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Jul 04 2013 - 08:00:03 PDT
