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

From: David A Case <>
Date: Fri, 5 Jul 2013 08:40:40 -0400

On Thu, Jul 04, 2013, Karl N. Kirschner wrote:
> 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"

Jason and Karl are correct: I misread the gaff.dat file. Note also that
Rob Woods has agreed to drop the "use by permission only" phrase above.


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Received on Fri Jul 05 2013 - 06:00:07 PDT
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