Dear Gromacs Users, Tsjerk,
the original file did not contain OXT, as you can see, it has O1 & O2, so I removed the O2 from the PDB and renamed O1 to OXT. 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 O1 CYS R 283 -26.993 93.593 -7.927 1.00 0.00 O ATOM 2844 O2 CYS R 283 -24.611 93.156 -8.027 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 sed -i '/^ATOM.*O2/d' DIMER.pdb Am i going wrong here....? the original PDB file is here : http://www.4shared.com/account/file/bTulGDPs/DIMER_FINAL.html 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, 12:22 PM 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://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-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. 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 -----Inline Attachment Follows----- -- 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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