Thanks
On Tue, Jun 18, 2013 at 10:44 PM, massimo sandal <deviceran...@gmail.com>wrote: > 2013/6/18 Hasni Arsad <hasni.ar...@gmail.com> > > > What should i do with this error massage: > > > > Google it. > > > > Program grompp, VERSION 4.6.2 > > Source code file: > > /home/hasni/Bioinformatics/gromacs-4.6.2/src/kernel/grompp.c, line: 563 > > > > Fatal error: > > number of coordinates in coordinate file (solv.gro, 50853) > > does not match topology (topol.top, 50816) > > For more information and tips for troubleshooting, please check the > GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > ______ > > > > > > > > solv.gro file > > > > 16268 > > 1MET N 1 3.978 6.462 2.460 > > 1MET H1 2 3.894 6.415 2.435 > > 1MET H2 3 4.057 6.411 2.426 > > 1MET H3 4 3.983 6.470 2.560 > > > > .. > > . > > . > > . > > . > > 275UNK H2 2869 9.769 6.981 4.477 > > 275UNK N1 2870 9.733 7.084 4.303 > > 275UNK C6 2871 9.725 7.203 4.240 > > 275UNK N6 2872 9.693 7.205 4.110 > > 275UNK H62 2873 9.675 7.119 4.062 > > 275UNK H61 2874 9.686 7.292 4.061 > > 276SOL OW 2875 0.569 1.275 1.165 > > 276SOL HW1 2876 0.476 1.268 1.128 > > 276SOL HW2 2877 0.580 1.364 1.209 > > 277SOL OW 2878 1.555 1.511 0.703 > > 277SOL HW1 2879 1.498 1.495 0.784 > > 277SOL HW2 2880 1.496 1.521 0.623 > > 278SOL OW 2881 1.743 0.618 0.856 > > 278SOL HW1 2882 1.776 0.712 0.856 > > . > > . > > > > 16267SOL OW50848 4.521 3.149 0.076 > > 16267SOL HW150849 4.437 3.148 0.130 > > 16267SOL HW250850 4.523 3.232 0.020 > > 16268SOL OW50851 7.487 8.525 5.886 > > 16268SOL HW150852 7.586 8.514 5.877 > > 16268SOL HW250853 7.447 8.439 5.918 > > > > > > topol.top file > > > > [ molecules ] > > ; Compound #mols > > Protein_chain_X 1 > > UNK 1 > > > > SOL 15993 > > > > > > > > > > > > > > > > > > > > > > On Tue, Jun 18, 2013 at 4:36 PM, Mark Abraham <mark.j.abra...@gmail.com > > >wrote: > > > > > GROMACS is not yet magic. You used an atom type not found in your force > > > field. Over to you. :-) > > > > > > Mark > > > On Jun 18, 2013 5:23 AM, "Hasni Arsad" <hasni.ar...@gmail.com> wrote: > > > > > > > Hi, > > > > > > > > I got this error massage when execute this command- grompp -f em.mdp > -c > > > > solvated.pdb -p topol.top > > > > > > > > > > > > > > > > Program grompp, VERSION 4.6.2 > > > > Source code file: ..../gromacs-4.6.2/src/kernel/toppush.c, line: 1336 > > > > > > > > Fatal error: > > > > Atomtype NPYL not found > > > > For more information and tips for troubleshooting, please check the > > > GROMACS > > > > website at http://www.gromacs.org/Documentation/Errors > > > > > > > > > > > > comment please!!!!! > > > > -- > > > > 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 > > > > > -- > > 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 > -- 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
