Re: AMBER: Antechamber functionality, MOL2 files

From: bigbrainstorm <>
Date: Wed, 13 Aug 2003 09:20:09 -0700

Thank you so much for your advice. Unfortunately, I do need to maintain
coordinates, but I will try the smile string suggestion. If I load the MOL2
file back into Sybyl and use that to split it into two separate files, will
it automatically renumber them and cause incompatibility with the pdb file I
load in, or is there a way to "freeze" the numbers assigned to each atom in
the structures if I were to delete half and save the other half into a new
MOL2 file in Sybyl? I'm afraid that I must use the original positional
coordinates for the two molecules in the MOL2 file, because it represents an
already properly relaxed conformation of the structure.

Yours Truly,

Zeve Akerling

----- Original Message -----
From: "Junmei Wang" <>
To: <>
Sent: Wednesday, August 13, 2003 8:06 AM
Subject: Re: AMBER: Antechamber functionality, MOL2 files

> 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
> 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.
> Junmei
> ===============================================================
> Dr. Junmei Wang
> Chemistry & Biophysics
> Encysive Pharmaceuticals
> 7000 Fannin, Houston TX 77030
> Tel: 713-5786649
> Email:
> Homepage: Http://
> ===============================================================
> "bigbrainstorm"
> <
>> To
> Sent by: <>
> owner-amber.scrip cc
> Subject
> AMBER: Antechamber functionality,
> 08/12/2003 09:50 MOL2 files
> PM
> Please respond to
> 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
> 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 - 17:53:01 PDT
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