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.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 12:17 PM > To: gmx-users@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> > > > > -- > View this message in context: > http://gromacs.5086.n6.nabble.com/polymer-duplicate-atoms- > tp5006328.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 -- 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
