[AMBER] questions about thermodynamic integration atom name and order

From: Yulin Huang <yulinhuang2007.gmail.com>
Date: Mon, 29 Oct 2012 10:35:55 -0400

Dear Amber users:
         I am performing binding free energy calculation for a kinase with
12 ligands using thermodynamic integration (AMBER11). It seems that the
atom names and orders for the corresponding atoms in these 12 ligands in
the initial setup have to be the same. Thus the
parm files and crd files generated after I use the antechamber, parmchk
could be the same
for the corresponding atoms. After that, the small mask (one or two atoms)
can be specified for calculations.

 I have manually made all the corresponding atom names the same. Now I am
trying to make the order the same. It is not an easy task. The way I do is
to put all the different atoms among 12 ligands at the end of ligand mol2
files. But I have to change all the connectivity part. I've tried to load
the mol2 file into software MOE and output the pdb file and then convert to
mol2 file. But the different atom such as O will be placed in the middle
of the mol2 file automatically. But I have to put the different atoms in
the end to make the corresponding atoms in the same order.

Does anyone has any ideas for this problems? Many thanks in advance.

Yulin "Joyce" Huang
Ph.D Candidate
Computational Chemistry (CADD)
Advisor: Dr. Robert C. Rizzo
State University of New York at Stony Brook
Stony Brook NY,11790
Office: (631)632-8519
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Received on Mon Oct 29 2012 - 08:00:04 PDT
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