[gmx-users] Re: .GRO and .TOP files editing

Vojtěch Spiwok Vojtech.Spiwok at vscht.cz
Tue Mar 6 11:30:39 CET 2007

> Message: 2
> Date: Tue, 6 Mar 2007 01:53:07 -0500
> From: "Karthikeyan Pasupathy" <karthik3k4md at gmail.com>
> Subject: [gmx-users] .GRO and .TOP files editing
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Message-ID:
> 	<7a3e1cb20703052253x36d86cd7iccce7f2b43dbf590 at mail.gmail.com>
> 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: spiwokv at vscht.cz
Web: biomikro.vscht.cz/groups/lab211/

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