The exact command is this:pdb2gmx -ff /home/user01/work/oplsaa.ff/ -f PTFE10.pdb -chainsep ter I have created this directory coping the oplssa.ff directory in share utilities (I'm an user not an administrator of the pc) and I cannot modify the original files. I attach the files .pdb, and the files oplssa.rtp ffgmx.rtp and residuetypes.dat that I have modified addying the new residues. (I have also modifed specbond.dat for the two bonds between internal residue and starting/terminal residues.
I don't know if I made mistakes or simply I use badly the command. Thanks for the fast reply.Luana. ----Messaggio originale---- Da: jalem...@vt.edu Data: 09/04/2013 19.02 A: "luanadelore...@libero.it"<luanadelore...@libero.it>, "Discussion list for GROMACS users"<gmx-users@gromacs.org> Ogg: Re: Re: [gmx-users] PTFE polymer chain Please keep the discussion on the gmx-users list. On Tue, Apr 9, 2013 at 12:55 PM, luanadelore...@libero.it <luanadelore...@libero.it> wrote: Hi Justin,thansk for the fast reply. The exact command is this:pdb2gmx -ff /home/user01/work/oplsaa.ff/ -f PTFE10.pdb -chainsep ter I have created this directory coping the oplssa.ff directory in share utilities (I'm an user not an administrator of the pc) and I cannot modify the original files. I attach the files .pdb, and the files oplssa.rtp ffgmx.rtp and residuetypes.dat that I have modified addying the new residues. (I have also modifed specbond.dat for the two bonds between internal residue and starting/terminal residues. I don know if I made mistakes or simply I use bad the command. The command is incorrect. The -ff flag takes only the prefix of the force field you're trying to use. Your command is going to look for a directory called /home/user01/work/oplsaa.ff/.ff, which of course does not exist. Put the custom oplsaa.ff directory in your working directory and issue pdb2gmx without the -ff flag. pdb2gmx will prompt you to choose the force field, allowing you to differentiate between oplsaa.ff in the working directory vs. the one in $GMXLIB. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- 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
