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

Mark Abraham Mark.Abraham at anu.edu.au
Wed Mar 7 01:16:58 CET 2007

Karthikeyan Pasupathy wrote:
> 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?

No, because this is a difficult area with user judgement required all 
the time... an automated tool would either not be very automated, or not 
be very useful.

The main solution is to read Chapter 5 in great detail, plan carefully, 
and get out your favourite text editor... using pdb2gmx and a modified 
.rtp file could well be the simplest solution, as suggested by another 


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