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.war...@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-boun...@gromacs.org [mailto:gmx-users- > boun...@gromacs.org] On Behalf Of cqgzc > Sent: Friday, 15 March 2013 6:20 PM > To: gmx-users@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> > > > > -- > View this message in context: > http://gromacs.5086.n6.nabble.com/polymer-duplicate-atoms- > tp5006328p5006334.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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