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

Luke Pestl luke.pestl at utoronto.ca
Tue Mar 6 16:12:05 CET 2007

Alternatively, you could define your monomers in the relevant ff???.rtp 
file so that pdb2gmx can build the polymer from residues.  You can use 
PRODRG to give you an idea of what charges you should assign to the 
atoms.  See section 5.5 of the manual for more information.


> 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 ?
> 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

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