AMBER Archive (2004)

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

From: Annette Höglund (hoeglund_at_informatik.uni-tuebingen.de)
Date: Mon May 31 2004 - 08:23:27 CDT

Dear All,

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).

Where should I start looking for the problem?
What should an "optimal" F_energy plot look like for an FEP?

Regards and thanks in advance,

Annette Höglund

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