Message: 2
Date: Tue, 6 Mar 2007 01:53:07 -0500
From: "Karthikeyan Pasupathy" <[EMAIL PROTECTED]>
Subject: [gmx-users] .GRO and .TOP files editing
To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset="iso-8859-1"
I have a polymer molecule (non-protein).
Therefore I could not use pdb2gmx and I tried to use PRODRG, but it could
process only small molecule.
I was suggested to run PRODRG with small molecule and manually stich the top
file.
Therefore I used a small molecule and obtained the .gro and .top files.
Now,
I have no clue how to stich this .top file.
Shouldn't I also make a .gro file on my own to proceed further ?
I sugest to use awk or some other text manipulation utility to build
coordinates and the topology manually
Is there any other alternative (other than PRODRG) to make these two files
or
Is there any software package/tool for file stitching?
Thanks,
Karthikeyan
---------------------------------------
Ing. Vojtech Spiwok, PhD.
Dept. of Biochemistry and Microbiology
Institute of Chemical Technology Prague
Technicka 3, Prague 6, 166 28,
Czech Republic
Tel: +420 22044 3028
Fax: +420 22044 5167
E-mail: [EMAIL PROTECTED]
Web: biomikro.vscht.cz/groups/lab211/
biomikro.vscht.cz/enzymologie
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