Re: AMBER: thermodynamic integration

From: David A. Case <>
Date: Thu, 24 May 2007 21:14:43 -0700

On Thu, May 24, 2007, Servaas Michielssens wrote:

> I was trying to do thermodynamic integration to calculate pKa values
> (in amber8). I made a perturbed paramter file in xleap, but I changed
> the parameters manual, not by the edit command in leap. I typed the
> changed values in the topology file under the flag pert_charge. I
> placed the anionic form in pert_charge and the neutral form in
> charge. I was confused about how to interpret the results. Can I use
> the results with the same sign or should I change sings?

I'm not sure that the question is clear enough. The DV/DL parameter (for
linear mixing) will be v1 - v0, where v1 is the potential energy with the
pert_charge and v0 is the potential energy with the regular charges. Since
you will have to do a small model compound anyway, run that and the sign of
the result should be obvious (the charged compound should have a much more
negative solvation energy than the neutral species.

...hope this helps...dac
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Received on Sun May 27 2007 - 06:07:36 PDT
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