[gmx-users] merge two PDBs
Hi everyone, can one still search the mailing list entries? I can't find it in the new site! A question: what would one want to do if he had a PDB file of a dimer and pdb2gmx couldn't analyse both of them, ending up giving some errors. I tried to separate two mers and then pdb2gmx'ed them getting nice topologies of each. But how can I merge them together again? the numbering will be messy. There should be some more human way for that :-) Editconf does not take two files and I don't want to put the other one at a random position since it needs to be just beside the other mer! What should one do at all, if one gets a NMR- based PDB which has the structure of more than one chemically equal species and wants to work with it? With Herzian thanks... Cheers, Peyman -- Peyman Yamin Institut fuer Strukturbiologie und Biophysik (ISB) ISB-3: Strukturbiochemie Forschungszentrum Juelich D-52425 Juelich Tel:(49)-2461-61-2875 Fax:(49)-2461-61-2023 mailto: p.yamin[at]fz-juelich.de Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] merge two PDBs
Peyman Yamin wrote: Hi everyone, can one still search the mailing list entries? I can't find it in the new site! I've posted this several times in the last few days: http://oldwww.gromacs.org/swish-e/search/search2.php A question: what would one want to do if he had a PDB file of a dimer and pdb2gmx couldn't analyse both of them, ending up giving some errors. I tried to separate two mers and then pdb2gmx'ed them getting nice topologies of each. But how can I merge them together again? the numbering will be messy. There should be some more human way for that :-) Editconf does not take two files and I don't want to put the other one at a random position since it needs to be just beside the other mer! What should one do at all, if one gets a NMR- based PDB which has the structure of more than one chemically equal species and wants to work with it? Concatenate the files using standard *nix utilities like cat, remove any repeated/unnecessary box information or REMARK lines, and use genconf to renumber. -Justin With Herzian thanks... Cheers, Peyman -- Peyman Yamin Institut fuer Strukturbiologie und Biophysik (ISB) ISB-3: Strukturbiochemie Forschungszentrum Juelich D-52425 Juelich Tel:(49)-2461-61-2875 Fax:(49)-2461-61-2023 mailto: p.yamin[at]fz-juelich.de Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] merge two PDBs
Hi, What error(s) do you get? /Erik Peyman Yamin skrev: Hi everyone, can one still search the mailing list entries? I can't find it in the new site! A question: what would one want to do if he had a PDB file of a dimer and pdb2gmx couldn't analyse both of them, ending up giving some errors. I tried to separate two mers and then pdb2gmx'ed them getting nice topologies of each. But how can I merge them together again? the numbering will be messy. There should be some more human way for that :-) Editconf does not take two files and I don't want to put the other one at a random position since it needs to be just beside the other mer! What should one do at all, if one gets a NMR- based PDB which has the structure of more than one chemically equal species and wants to work with it? With Herzian thanks... Cheers, Peyman -- Peyman Yamin Institut fuer Strukturbiologie und Biophysik (ISB) ISB-3: Strukturbiochemie Forschungszentrum Juelich D-52425 Juelich Tel:(49)-2461-61-2875 Fax:(49)-2461-61-2023 mailto: p.yamin[at]fz-juelich.de Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
