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.
Luke
Message: 2
Date: Tue, 6 Mar 2007 01:53:07 -0500
From: "Karthikeyan Pasupathy" <[EMAIL PROTECTED]>
Subject: [gmx-users] .GRO and .TOP files editing
To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Message-ID:
<[EMAIL PROTECTED]>
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
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
