Re: AMBER: thermodynamic integration

From: Servaas Michielssens <>
Date: Fri, 25 May 2007 09:23:21 +0200

My confusion came from page 132 and 289 of the AMBER manual, where
lambda values seem to be switched. If in my prmtop file the charges of
the anion are under pert_charge and the neutral ones under charge, is
the value of DV/DL in my output file then the derivative of the
function seen from anion to neutral or oppositie. If this is from
neutral to anion this is the value to use to do the integration, in
the other case I should change signs.
So the problem is if in the prmtop file anion is in the pert_charge
how does amber caculates DV/DL.

kind regard,


Quoting "David A. Case" <>:

> 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 - 06:07:37 PDT
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