[gmx-users] grompp error

[massimo sandal]

2013/6/18 Hasni Arsad <hasni.arsad at gmail.com>

> What should i do with this error massage:
>

Google it.


> 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.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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