AMBER Archive (2004)

Subject: Re: AMBER: program compatibility

From: David A. Case (case_at_scripps.edu)
Date: Mon May 31 2004 - 00:05:15 CDT

On Mon, May 31, 2004, hj zou wrote:

> I have run molecular dynamics simulation of a system by using program
> GROMACS and many analysises are performed.As a part of analysis,now I
> want to calculate the binding free energy of the system by using MMPB/SA
> in AMBER.What should I do?Maybe there are two ways:

> Are there any other better ways to solve this problem?

One third possibility is to carry out the analysis using GROMACS itself (and a
separate Poisson-Boltzmann program if GROMACS doesn't have one, such as UHBD,
Delphi, MEAD)

The mm_pbsa script in Amber is helpful in "automating" the process of
collecting snapshots and doing statistics, but there is nothing it does
that cannot also be done by hand (which is how such calculations were
originally carried out). In this way, everything uses the same (GROMACS)
force field.

This is just a thought; the other options you suggested also have pros and
cons.

...good luck...dac

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