[gmx-users] Re: polymer duplicate atoms

[Dallas Warren]

That is something you will have to sort out, since you have all the files (in and out) and know the molecule(s) you are processing.  You have provided insufficient information to help without having to spend a significant amount of time trying to work what it all means.

If pdb2gmx is telling you that there is a strange residue in your .pdb file, then your formatting or numbering that you have put in there is not consistent with what pdb2gmx is expecting to get the "correct" output.

Have you attempted to get it work using a polymer of the shortest possible length?  Say two terminals?  Then added one, two etc of the middle residues?  When starting something new and complex, you should start with something simple to ensure things are behaving as you expect them to, and if not it is much easier to work out why.  Then you make things more and more complex, until you are up to where you want to be.

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 6:20 PM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Re: polymer duplicate atoms
> 
> Dear Dallas
> 
>     Thanks for your reply. I followed the way of you said to modify the
> residue number in sequence. It generated a complete sturctural file
> (conf.gro) without deleting the duplicate atoms. However, it denoted
> another
> strange structure which contained many seperated residue
> —(CH2-CF2-CF2-CFCl)—
> It's not the polymer structure.
> f2311-new.pdb
> <http://gromacs.5086.n6.nabble.com/file/n5006334/f2311-new.pdb>
> 
> 
> 
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> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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