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