[AMBER] Alanine scanning

From: Guenegou, Guillaume [ORDFR] <GGUENEGO.ITS.JNJ.com>
Date: Fri, 10 Jun 2011 15:51:02 +0200

Dear all,

I work with amber11 and AmberTools1.5.

I want to use alanine scanning protocol with mm_pbsa.pl and I get the
following error message:

"Prmtop ../../leap/FABI_C01_ChainD_2_wat/FABI_C01_ChainD_2.top and
coord.file ./1_2_com.crd.1 have different atom numbers
         For details see:
at /clu01/applic/amber11/src/mm_pbsa/mm_pbsa_calceneent.pm line 1137."

I guess this different atom number comes from the fact that the
coord.file contains mutant residues, so the number of atoms is different
from the one in topology file.

Does it mean I have to generate a topology file with mutant residues
before launching alanine scanning?
In that case, I don't understand the interest of alanine scanning
protocol with mm_pbsa.pl

If someone has an idea...


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Received on Fri Jun 10 2011 - 07:00:04 PDT
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