RE: [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: xiaowu...@hotmail.com
To: gmx-users@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
xiaowu...@hotmail.com
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Re: [gmx-users] Now there are 16 atoms. Deleted 304 duplicates.

[David van der Spoel]

xiaowu...@hotmail.com wrote:
 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?
  
The information you are sending here is not complete. How were termini
treated, hw was pdb2gmx invoked?
How do the building blocks in the rtp file and hdb file look like?

 Best regards,
 Chaofu Wu
 xiaowu...@hotmail.com mailto:xiaowu...@hotmail.com
 
 
 
 
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell  Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
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