AMBER Archive (2003)

Subject: Re: AMBER: Antechamber functionality, MOL2 files

From: Junmei Wang (JWang_at_encysive.com)
Date: Wed Aug 13 2003 - 11:28:03 CDT

I just thought out another idea, why not use leap! You may use antechamber
to convert that mol2 file into pdb and load it into leap. From the edit
window, you can delete some atoms and only keep one molecule and save it in
pdb format (savepdb). Do this for each molecule in that file. By this way,
you both keep coordinates and atom names.

Best

Junmei

===============================================================
Dr. Junmei Wang
Chemistry & Biophysics
Encysive Pharmaceuticals
7000 Fannin, Houston TX 77030
Tel: 713-5786649
Email: jwang_at_tbc.com
Homepage: http://sigyn.compchem.ucsf.edu/members/jmwang/index.html
===============================================================

                                                                           
             "bigbrainstorm"
             <bigbrainstorm_at_co
             mcast.net> To
             Sent by: <amber_at_scripps.edu>
             owner-amber_at_scrip cc
             ps.edu
                                                                   Subject
                                       Re: AMBER: Antechamber
             08/13/2003 11:20 functionality, MOL2 files
             AM
                                                                           
                                                                           
             Please respond to
             amber_at_scripps.edu
                                                                           
                                                                           

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" <JWang_at_encysive.com>
To: <amber_at_scripps.edu>
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
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.
>
> Junmei
>
> ===============================================================
> Dr. Junmei Wang
> Chemistry & Biophysics
> Encysive Pharmaceuticals
> 7000 Fannin, Houston TX 77030
> Tel: 713-5786649
> Email: jwang_at_tbc.com
> Homepage: http://sigyn.compchem.ucsf.edu/members/jmwang/index.html
> ===============================================================
>
>
>
>
> "bigbrainstorm"
> <bigbrainstorm_at_co
> mcast.net>
To
> Sent by: <amber_at_scripps.edu>
> owner-amber_at_scrip
cc
> ps.edu
>
Subject
> AMBER: Antechamber functionality,
> 08/12/2003 09:50 MOL2 files
> PM
>
>
> Please respond to
> amber_at_scripps.edu
>
>
>
>
>
>
>
> 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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