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

From: Carlos Simmerling <>
Date: Mon, 31 May 2004 13:56:24 -0400

you originally said you tried asp-->ala, that is why dac mentioned decoupling.
now you say you are doing asn-->asp. which is right?
also, since you are removing a formal charge, it is not at
all surprising that your free energy curve differs from val-->ala
where the only change is really size.
  ----- Original Message -----
  From: Sébastien Osborne
  Sent: Monday, May 31, 2004 1:51 PM
  Subject: Re: AMBER: FEP error/early termination - why?

  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 - 19:53:01 PDT
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