Please keep GROMACS usage questions on the gmx-users mailing list. Nobody here is a private tutor :-)
The error messages you are getting are self-explanatory. You need to think about why they are arising. Perhaps do some tutorials to get a feel for normal workflows, and how best to modify them to suit your needs. Mark On Tue, Jun 18, 2013 at 10:57 AM, Hasni Arsad <[email protected]> wrote: > > > ---------- Forwarded message ---------- > From: Hasni Arsad <[email protected]> > Date: Tue, Jun 18, 2013 at 4:55 PM > Subject: Re: [gmx-users] grompp error > To: Discussion list for GROMACS users <[email protected]> > > > 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, 16268) > 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 > > ______ > > Attach is my topol.top and solv.gro. > > > > > On Tue, Jun 18, 2013 at 4:36 PM, Mark Abraham <[email protected]>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" <[email protected]> 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 [email protected] >> > 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 [email protected]. >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> -- >> gmx-users mailing list [email protected] >> 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 [email protected]. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
