Re: AMBER: Antechamber functionality, MOL2 files

From: Junmei Wang <>
Date: Wed, 13 Aug 2003 10:06:47 -0500

I don't think antechamber can generate a single prep file for two
molecules. If you don't want keep the atom names in that mol2 file, you may
load the mol2 file into sybyl and copy each residue into a new molecular
area and save them separately. Or if you even don't care the coordinates,
you may convert the mol2 file into a smile string and then dissect it
(molecules are separated by '.' in smile string) and then convert each of
them back to mol2 file.


Dr. Junmei Wang
Chemistry & Biophysics
Encysive Pharmaceuticals
7000 Fannin, Houston TX 77030
Tel: 713-5786649
Homepage: Http://

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                                       AMBER: Antechamber functionality,
             08/12/2003 09:50 MOL2 files
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Dear AMBER community,

    I am using Amber 7 on Linux and O2 SGI machines. I am attempting to
simulate a system consisting of two separate but catenated organic
molecules. My starting structure is a MOL2 file. I am using babel to
convert this into a pdb file and load that into XLEAP for positional
coordinates. I am having some difficulty generating prep
files. Unfortunately, I can't seem to get Antechamber to read both
molecules simultaneously, and I can't split the MOL2 file into two separate
files because the atomic numbering scheme in the MOL2 seems to "mix" both
molecules together, and there is no single point of division. The whole
system is on the order of >450 heavy atoms, so I would really prefer to
avoid hand editing.
    Is there any way that Antwechamber could be used to generate a single
prep file out of two molecules in a single file? Alternatively, does
anyone know of a program that would allow me to renumber the MOL2 file so
that I could split it up manually?
I would appreciate any help you could give me.

Yours Truly,

Zeve Akerling, UCLA, Undergraduate Summer Research Program.

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Received on Wed Aug 13 2003 - 16:53:01 PDT
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