Re: [AMBER] questions about thermodynamic integration atom name and order

From: Jodi Ann Hadden <>
Date: Tue, 30 Oct 2012 20:48:16 +0000

Hi Joyce,

This seems like an unnecessary complication.

Since you are doing TI in AMBER11, I assume you are using soft core potentials instead of the dummy atom method, and you have separate topology files that represent the lambda=0 and lambda=1 end states. In this case, you only have to make sure the common atoms from each state are in the same order in the two separate files, that is, the atoms that are not going in your scmask. If the common atoms are in the same relative order, but just have scmask atoms in between them, that is fine. Everything else just has to be the same ignoring scmask atoms. Since your scmask is only one or to atoms, this should be pretty easy to ensure without excessive file manipulation. You don't have to move the ligand differences to the end of the file as long as you are specifying them in your scmask.

Hope this helps,

Jodi Hadden
Complex Carbohydrate Research Center
University of Georgia

On Oct 29, 2012, at 10:35 AM, Yulin Huang <<>> wrote:

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 Tue Oct 30 2012 - 14:00:03 PDT
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