RE: AMBER: Amber 8: questions about free energy perturbation

From: case <>
Date: Mon, 12 Sep 2005 00:29:15 -0700

>===== Original Message From Angela Liu =====

>1) In the older version of Amber (such as Amber 7 and
>Amber 6), "gibbs" was the routine that is used to
>calculate free energy perturbations. It uses "dual
>topology" so that the unperturbed and perturbed
>systems can have unique atoms to themselves. Kollman
>indicated in his 1993 Chem Rev review that dual
>topology methods often suffer from poor convergence
>problems. Is this the reason why this "dual topology"
>approach was no longer supported in Amber?

Someone may wish to correct me, but I don't believe that true "dual topology"
calculations have ever been supported in Amber.

>So if I DO want to calculate the free energy of a
>mutation, say from purine to pyrimidine (a problem
>clearly explained in Kollman's 1993 review with
>"single topology"), is there no way Amber 8 can allow
>this to be done?

Sure, since we do use a "single topology" approach. There is a tutorial on
changing toluene to nothing, which is not conceptually different from changing
a purine to a pyrimidine.

>3) How can I get hold of the source code of "gibbs" in
>Amber 7 or 6?

You have already indicated that you have access to the source code, so
I don't understand the problem. If there are compilation problems, please
check the mailing archives for similar problems, and/or give more specific


David A. Case | e-mail:
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 |

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Received on Mon Sep 12 2005 - 08:53:00 PDT
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