AMBER Archive (2007)

Subject: Re: AMBER: gibbs problems

From: David A. Case (case_at_scripps.edu)
Date: Wed Oct 31 2007 - 22:09:35 CST

On Wed, Oct 31, 2007, JAVIER PEREZ wrote:
>
> I am working with FEP calculations using gibbs. When a FEP calculation
> finishes, I obtain a .trj file, a .mst file, an .out file and a .rst file
> which contains information about the final state of the perturbation. I
> would like to use that restart file as a starting point for a Molecular
> dynamic simulation. I think that I should use the perturbated topology file
> created in xleap and used previously for FEP calculations.
>
> My problem is that I do not know which flags I should add in my molecular
> dynamics input file to run a simulation using the structure with
> perturbation. I have carefully read the amber manual. However, it does not
> clarify my doubts.

Gibbs is a really old program. I think if you run the system, asking for
thermodyanmic integration, and setting lambda to 1, you will get a simulation
with the perturbed system. But be sure to check carefully that you are
getting what you want. It would probably be better to re-make a standard
(non-pert) prmtop file, and use sander or pmemd (hopefully with a more recent
version of Amber) in order to carry out a standard MD simulation.

...good luck...dac

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