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

From: Daniel Roe <>
Date: Wed, 31 Oct 2012 09:43:24 -0600


You could try the 'atommap' command in Cpptraj, which employs a simple
algorithm to reorder a target structure according to an origin
structure based on bonding patterns. As long as your ligand is not too
large (<100 atoms or so) and the # of atoms in target and origin are
fairly close the algorithm works pretty well.

Say your target is target.pdb and the origin you want it to map to is
origin.pdb; the command sequence is:

parm target.pdb [target]
reference target.pdb parm [target]
parm origin.pdb [origin]
reference origin.pdb parm [origin]

atommap target.pdb origin.pdb mapout atommap.dat # This creates the atom map

trajin target.pdb parm [target]
trajout reordered.pdb parm [target] # This will print out target.pdb
reordered according to origin.pdb

Hope this helps, let me know if you try it and run into problems.


On Wed, Oct 31, 2012 at 2:35 AM, <> wrote:
> 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
> case.
> 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,
> Thomas
> 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
>> _______________________________________________
>> AMBER mailing list
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Wed Oct 31 2012 - 09:00:03 PDT
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