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. (Did you perhaps try to use Amber
atom types?) Also, the C6 and C8 atoms in your pdb file don't have the
right number of hydrogens (did the email get truncated?)
...dac
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Received on Thu Jul 04 2013 - 06:30:02 PDT
