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

[Berk Hess]

Hi,

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.

Berk

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."








Dear,
  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
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