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
--
==================================================================
David A. Case | e-mail: case.scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Mon May 31 2004 - 18:53:00 PDT
