Re: AMBER: Questions about mm_pbsa and alanine scanning

From: Natasja Brooijmans <>
Date: Tue, 15 Jul 2003 13:42:40 -0700 (PDT)

When you do alanine scanning, you need to generate topology files for the
mutant system with leap before you run the mmpbsa scripts.

Good luck,


Natasja Brooijmans, Ph.D.
Visiting Post-Doctoral Scholar
Kuntz Laboratory
Department of Pharmaceutical Chemistry
University of California, San Francisco
San Francisco, CA 94143-2240
phone: 415-476 3986
fax: 415-502 1411

On Tue, 15 Jul 2003, Haizhen Zhong wrote:

> Dear Amber users,
> I'm very interested in using the computational Alanine scanning technique
> described in mm_pbsa munual. Yet I've found it's hard to understand some
> of the scripts in the mm_pbsa file. I've had the correct topology files
> for the mutants. According to the definitions of "MUTANT_ATOM1",
> input files exactly according to the definitions. Unfortunately, after
> running mm_pbsa, I got "FATAL: Topology and coord files do not match" in
> my anal_complex.1.out file. After checking the coordinate files from
> complex, protein, and ligand (a small peptide, mutation was on this small
> peptide) with respective prmtop files, I found the atom numbers were
> different between the crd file and the prmtop file. I believe the problem
> lies in the definition of the above four variables. Among these four,
> "MUTANT_ATOM1" and "MUTANT_REFERENCE" are clear and easy to understand.
> Therefore the most problem may be in the definition of "MUTANT_ATOM2" or
> "MUTANT_KEEP" (especially "MUTANT_KEEP").
> Worthy to mention is that if you look at the example provided in the
> amber6 mm_pbsa for the alanine scanning for residues in p53, you can find
> the numbers for the above four variables contradictory with each other in
> terms of Thr18, Phe19 and Trp23 mutated to Ala (line 584 to line 596 in
> mm_pbsa script in amber6 version).
> Can anyone clarify my confusion and help me with the alanine scanning
> using mm_pbsa?
> Thank you very much for your help!
> Haizhen
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Received on Tue Jul 15 2003 - 21:53:01 PDT
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