What should i do with this error massage: 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