AMBER Archive (2004)

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

From: David A. Case (case_at_scripps.edu)
Date: Mon May 31 2004 - 12:33:08 CDT

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
> the arror message: "ERROR TERMINATION DUE TO SHAKE OR TORCON"
> 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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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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