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
poster.
Mark
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