[gmx-users] grompp error

[Mark Abraham]

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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>