[gmx-users] polymer duplicate atoms

[Dallas Warren]

The residue number is not incrementing in your coordinate file (it stays as 1), so it thinks it is all the same residue.

Catch ya,

Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
+61 3 9903 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail. 


> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> bounces at gromacs.org] On Behalf Of cqgzc
> Sent: Friday, 15 March 2013 12:17 PM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] polymer duplicate atoms
> 
> Hi
> I use the pdb2gmx to generate topology file of polymer
> f2311(fluororubber)
> with the incorrect information of GROMACS structural file (conf.gro).
> There
> are 680 atoms in my input (.pdb) file. But, 660 atoms are deleted in
> conf.gro file because of duplicate atoms. The printed message as
> follow:
>   <http://gromacs.5086.n6.nabble.com/file/n5006328/info.jpg>
> Residues Fre, Fbg and Fen denote repeat unit., head and tail part of
> polymer, respectively. How can I obtain the correct file structure
> (conf.gro) to avoid deleting duplicate atoms. Any help with my best
> appreciation. Attachment is my pdb file.
> f2311.pdb <http://gromacs.5086.n6.nabble.com/file/n5006328/f2311.pdb>
> 
> 
> 
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