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

From: <>
Date: Wed, 31 Oct 2012 04:35:56 -0400 (EDT)

Hi Joyce,

in case the ligand files come from some third party software that does
completely mix up the atom order (e.g. because an additional group changes
the numbering order in a ring), there is probably really no way around
rebuilding them by hand.

When ligands are fairly similar it may help to draw their common core in
xleap, save that fragment and then build each ligand from the fragment and
saving it as mol2. I think the common atom order will be the same in that

Take care, when you run such a ligand through antechamber, e.g. for
charges, it may reorder the atoms again. Some hand manipulation/checking
is certainly involved in this, I think there is no reliable automated way
yet. This may change in Amber13, though...

Kind Regards,


On Tue, October 30, 2012 4:48 pm, Jodi Ann Hadden wrote:
> 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
> 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
> _______________________________________________
> AMBER mailing list
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Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Wed Oct 31 2012 - 02:00:03 PDT
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