[gmx-users] "Now there are 16 atoms. Deleted 304 duplicates."

Berk Hess gmx3 at hotmail.com
Mon Mar 16 12:37:35 CET 2009


My guess would be that you used the same residue number for all your 20 repeat units.
In that case pdb2gmx find 304 duplicate atoms in a single residue and deletes them.


From: xiaowu759 at hotmail.com
To: gmx-users at gromacs.org
Date: Sat, 14 Mar 2009 16:06:07 +0800
Subject: [gmx-users] "Now there are 16 atoms. Deleted 304 duplicates."

  As a small test, I want to simulate polystyene(PS) 
using GROMACS. Firstly, I obtain a pdb file of a PS chain consisting of 
20 repeating unit(320 atoms totally ) and add the STY residues to the 
.rtp files. while running pdb2gmx, the procedure was finished "successfully". 
but I find that only 16 atoms are in the generated .gro and .top files. Have you 
met this strange thing? Or tell me what I should do with it?
Best regards,
Chaofu Wu
xiaowu759 at hotmail.com
What can you do with the new Windows Live? Find out
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