Hi Nahren, Can you paste your actual command line where you used sed?
Cheers, Tsjerk On Tue, Sep 7, 2010 at 12:11 PM, nahren manuel <meetnah...@yahoo.com> wrote: > Dear Gromacs Users, > > thanks for all your suggestions. > > Tsjerk, I did try your idea, but unfortunately doesn't seem to work. > > the pdb file is shared here : > http://www.4shared.com/account/file/ijofD83b/DIMER.html > > newpdb2gmx -f DIMER.pdb -chainsep interactive -ignh > > Fatal error: > Atom OXT in residue CYS 283 was not found in rtp entry CYS with 11 atoms > while sorting atoms. > . > > > Part of the file is pasted below: > > ATOM 2836 N CYS R 283 -27.431 91.636 -6.099 1.00 > 0.00 N > ATOM 2837 H CYS R 283 -27.855 90.779 -6.392 1.00 > 0.00 H > ATOM 2838 CA CYS R 283 -26.033 91.780 -6.514 1.00 > 0.00 C > ATOM 2839 CB CYS R 283 -25.500 90.433 -7.060 1.00 > 0.00 C > ATOM 2840 SG CYS R 283 -25.121 89.114 -5.829 1.00 > 0.00 S > ATOM 2841 HG CYS R 283 -24.270 89.566 -4.957 1.00 > 0.00 H > ATOM 2842 C CYS R 283 -25.867 92.922 -7.562 1.00 > 0.00 C > ATOM 2843 OXT CYS R 283 -26.993 93.593 -7.927 1.00 > 0.00 O > ATOM 2845 N LYS B 284 -23.431 108.789 63.478 1.00 > 0.00 N > ATOM 2846 H1 LYS B 284 -23.779 109.339 64.238 1.00 > 0.00 H > ATOM 2847 H2 LYS B 284 -23.156 109.392 62.730 1.00 > 0.00 H > > > Best, > nahren > > --- On *Tue, 9/7/10, Tsjerk Wassenaar <tsje...@gmail.com>* wrote: > > > From: Tsjerk Wassenaar <tsje...@gmail.com> > Subject: Re: [gmx-users] pdb2gmx -chainsep vs -merge > To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> > Date: Tuesday, September 7, 2010, 11:14 AM > > Hi, > > > One work-around for the -chainsep situation you've observed is to remove > or rename the terminal oxygen atoms (OXT) that pdb2gmx is complaining about > when it tries to merge the chains. It should be taking care of that itself, > but handling it yourself might help. pdb2gmx can probably rebuild the > carboxyl oxygen. Keeping (one of the) OXT atoms and renaming it to "O" > (keeping the fixed-column format correct) might be needed. > > There should be only one OXT per chain. Removing those seems like a good > idea: > > sed -i '/^ATOM.*OXT/d' file.pdb > (Remove all lines starting with ATOM and containing OXT, in the file) > > Hope it helps, > > Tsjerk > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Molecular Dynamics Group > Groningen Institute for Biomolecular Research and Biotechnology / > University of Groningen > The Netherlands > -- > > gmx-users mailing list > gmx-users@gromacs.org<http://mc/compose?to=gmx-us...@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<http://mc/compose?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 > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology / University of Groningen The Netherlands
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