[gmx-users] grompp error

[Hasni Arsad]

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, 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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