Thanks, Finally I managed to run MD of protein-ligand complex after a few trial of tutorial....
On Tue, Jun 18, 2013 at 5:06 PM, Mark Abraham <[email protected]>wrote: > 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 > -- 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
