Re: [AMBER] Abnormal simulation in the sulfonic acid group.

From: Karl N. Kirschner <>
Date: Thu, 4 Jul 2013 16:58:43 +0200 (CEST)


  Indeed, antechamber assigns an "ho" atom type to these R-SO3H systems (at least it did for benzenesulfonic acid), and thus epislon and R of 0.0. The behavior that is seen then in the MD simulation is identical to that seen in hydroxyl groups present in carbohydrates. One quick and approximate solution would be to add small terms to this LJ parameter, like the Glycam group (Tessier and Woods) did recently:

"Ho 0.2000 0.0300 M.B. Tessier 2011, use by permission only"


----- Original Message -----
From: "Jason Swails" <>
To: "AMBER Mailing List" <>
Sent: Thursday, July 4, 2013 4:42:09 PM
Subject: Re: [AMBER] Abnormal simulation in the sulfonic acid group.

On Thu, Jul 4, 2013 at 9:08 AM, David A Case <>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 M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Thu Jul 04 2013 - 08:30:02 PDT
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