Re: [AMBER] Topology Reorder for EVB

From: Jason Swails <>
Date: Mon, 7 Dec 2009 13:59:23 -0500

As far as I know, antechamber should be able to create mol2 files just fine
(I've done it on several occasions). There may be some kind of error on the
antechamber system call perhaps? What command are you using to execute
antechamber? (I've likewise been able to use babel to produce mol2 files,
which command are you using for that as well?)

Another way you may try doing this with an amber prep file is to save it as
a cartesian prep file (prepc instead of prepi). In this case, the residue
is not stored as a zmat so the order of the atoms no longer matters. Thus,
you may be able to reorder the prep files to match just by swapping lines.
Someone else on the list may correct me here, but the point remains that
antechamber should be able to create the mol2 if that format will work
better for you.

Good luck!

On Mon, Dec 7, 2009 at 10:58 AM, Andrea Coletta <> wrote:

> Hello,
> I was planning to use the EVB facility in Amber9 to explore an
> intramolecular proton transport.
> As I've read on the manual, I need two topologies for the two diabatic
> states, but I also need the atom order to be the same and I can't figure it
> out how to do that.
> I have two .gzmat, containing the output of QM optimization for each state,
> in which the atoms' order is the same.
> When I process they with antechamber to obtain the prep, the order in the
> output is not the same: the proton is in a different position, in
> consequence of the different topology (the hydrogen pass from a group to
> another, and if I try to change manually the order, I get a wrong topology).
> I've googled and found somebody who said to use a .mol2 instead of .prep...
> but i can't obtain a mol2 neither with antechamber (segmentation fault!) nor
> openbabel (no output)...
> Somebody can help me?
> Thanks
> Andrea Coletta
> UniversitÓ degli Studi di Roma "Tor Vergata"
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Mon Dec 07 2009 - 11:30:03 PST
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