AMBER: Questions about mm_pbsa and alanine scanning

From: Haizhen Zhong <>
Date: Tue, 15 Jul 2003 16:34:32 -0400 (EDT)

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!


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Received on Tue Jul 15 2003 - 21:53:01 PDT
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