Re: AMBER: FEP error/early termination - why?

From: Sébastien Osborne <>
Date: Mon, 31 May 2004 13:51:15 -0400

what exactly do you mean by "decoupling the charge change and the VDW
change"? I am trying to do the following perturbation: ASN --> ASP
where the NH2 part of ASN becomes O. In the process, I am perturbing
the hydrogen atoms to dummy atoms. Are you saying it is better to
perform 2 runs, a first run where the hydrogen becomes "charged" dummy
atoms (no change on the charge in the run) followed by a second run
where the charge on the dummy atoms become 0?

Thanks for the help.

Sebastien Osborne
University of Ottawa

David A. Case wrote:

>On Mon, May 31, 2004, Annette Höglund wrote:
>>I have tried to run an initial free energy perturbation for a ASP->ALA
>>sidechain in a protein-DNA complex (after minimization and
>>equilibration) using a similar gibbs input as in the val-to-ala tutorial.
>>For this particular sidechain the FEP terminates after about 75% with
>>When I plot the F_energy it seems to be a "concave" rather than "convex"
>>curve (as in the tutorial).
>Are you decoupling the charge change from the van der Waals change? (Not
>doing that _could_ lead the symptom you cite, but that is just a guess.) Be
>sure to run the ASP->ALA change in water first (since it is simpler, and can
>help you debug your scripts), before trying it in the protein/DNA system.
>...good luck...dac

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Received on Mon May 31 2004 - 19:53:00 PDT
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