[gmx-users] grompp error

[Hasni Arsad]

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 <mark.j.abraham at gmail.com>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 <hasni.arsad at gmail.com>
> wrote:
>
> >
> >
> > ---------- Forwarded message ----------
> > From: Hasni Arsad <hasni.arsad at gmail.com>
> > Date: Tue, Jun 18, 2013 at 4:55 PM
> > Subject: Re: [gmx-users] grompp error
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >
> >
> > 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 <mark.j.abraham at 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.arsad at 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!!!!!
> >> > --
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