[gmx-users] number of coordinates in coordinate file (system.gro, 10019) does not match topology (topol.top, 17093)

swati rana swati.rana088 at gmail.com
Thu Mar 21 07:00:25 CET 2013


yes its POPC at the top and SOL at the bottom. But the atoms names are not
same that is the problem. ...

I am pasting the part of the gro file from where the problem has started.
At 129 position the atom name is OW1 where as in topol file it is OW.
Please guide me what should be done.

 128POP    C50 6654   4.864  -0.191   3.551
  128POP    CA1 6655   5.688   0.221   3.577
  128POP    CA2 6656   5.641   0.199   3.433
  129SOL    OW1 6657   5.223   1.492   0.817
  129SOL    HW2 6658   5.129   1.491   0.783
  129SOL    HW3 6659   5.277   1.423   0.769
  130SOL    OW1 6660   3.403   3.481   1.092
  130SOL    HW2 6661   3.313   3.523   1.107
  130SOL    HW3 6662   3.391   3.383   1.076
  131SOL    OW1 6663   3.852   2.274   0.985
  131SOL    HW2 6664   3.949   2.292   0.969
  131SOL    HW3 6665   3.811   2.353   1.030
  132SOL    OW1 6666   2.283   4.574   6.734
  132SOL    HW2 6667   2.231   4.637   6.675
  132SOL    HW3 6668   2.364   4.543   6.685
  133SOL    OW1 6669   2.569   2.428   5.841
  133SOL    HW2 6670   2.623   2.469   5.914
  133SOL    HW3 6671   2.629   2.372   5.783
  134SOL    OW1 6672   4.126   0.240   5.606
  134SOL    HW2 6673   4.180   0.312   5.562
  134SOL    HW3 6674   4.182   0.159   5.620
  135SOL    OW1 6675   5.968   3.911   5.734
  135SOL    HW2 6676   5.903   3.964   5.679
  135SOL    HW3 6677   6.042   3.878   5.675
  136SOL    OW1 6678   5.884   2.082   0.044
  136SOL    HW2 6679   5.824   2.156   0.076
  136SOL    HW3 6680   5.860   2.060  -0.051
  137SOL    OW1 6681   3.169   2.752   1.170
  137SOL    HW2 6682   3.250   2.714   1.214
  137SOL    HW3 6683   3.169   2.727   1.073
  138SOL    OW1 6684   5.521   5.906   6.408
  138SOL    HW2 6685   5.601   5.848   6.422
  138SOL    HW3 6686   5.480   5.927   6.497
  139SOL    OW1 6687   5.333   3.675   1.289
  139SOL    HW2 6688   5.387   3.677   1.205
  139SOL    HW3 6689   5.338   3.584   1.330
  140SOL    OW1 6690   3.167   5.794   0.240
  140SOL    HW2 6691   3.077   5.820   0.204
  140SOL    HW3 6692   3.237   5.854   0.203

Thanks in advance...

Swati


On Thu, Mar 21, 2013 at 11:18 AM, Emanuel Birru <Emanuel.Birru at monash.edu>wrote:

> If the atom names in your gro file and in the top file are the same then I
> suggest to check how the sequence of the atoms looks like in your gro file.
> Is it POPC at the top and the water at the bottom as your topology
> suggested? If not swap them in the molecule section.
>
>  [ molecules ]
> ; molecule name nr.
> POPC 128 ???
> SOL 2460  ???
>
> Cheers,
> EB
>
>
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of swati rana
> Sent: Thursday, 21 March 2013 4:37 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] number of coordinates in coordinate file
> (system.gro, 10019) does not match topology (topol.top, 17093)
>
> Dear Justin,
>
> I am facing another problem i.e. IN removing the periodicity of the
> downloaded popc128a.pdb file.
>
> Warning: atom name 6673 in topol_popc.top and popc128a.gro does not match
> (HW1 - HW2)
> Warning: atom name 6674 in topol_popc.top and popc128a.gro does not match
> (HW2 - HW3)
> Warning: atom name 6675 in topol_popc.top and popc128a.gro does not match
> (OW - OW1)
> Warning: atom name 6676 in topol_popc.top and popc128a.gro does not match
> (HW1 - HW2)
> (more than 20 non-matching atom names)
>
> WARNING 1 [file topol_popc.top, line 31]:
>   7380 non-matching atom names
>   atom names from topol_popc.top will be used
>   atom names from popc128a.gro will be ignored
>
> This question has been asked by another person as well and in case the
> solution he suggested worked. But in my case everything in the pdb file is
> okie though i am getting this error. Please suggest what should be done.
>
> spc.itp file is like this:
>
> [ moleculetype ]
> ; molname    nrexcl
> SOL        2
>
> [ atoms ]
> ;   nr   type  resnr residue  atom   cgnr     charge       mass
> #ifndef HEAVY_H
>      1     OW      1    SOL     OW      1      -0.82   15.99940
>      2      H      1    SOL    HW1      1       0.41    1.00800
>      3      H      1    SOL    HW2      1       0.41    1.00800
> #else
>      1     OW      1    SOL     OW      1      -0.82    9.95140
>      2      H      1    SOL    HW1      1       0.41    4.03200
>      3      H      1    SOL    HW2      1       0.41    4.03200
> #endif
>
> #ifndef FLEXIBLE
> [ settles ]
> ; OW    funct    doh    dhh
> 1    1    0.1    0.16330
>
> [ exclusions ]
> 1    2    3
> 2    1    3
> 3    1    2
> #else
> [ bonds ]
> ; i    j    funct    length    force.c.
> 1    2    1    0.1    345000    0.1     345000
> 1    3    1    0.1    345000    0.1     345000
>
> [ angles ]
> ; i    j    k    funct    angle    force.c.
> 2    1    3    1    109.47    383    109.47    383
> #endif
>
> And topol file is:
>
> ;
> ;    File 'topol_popc.top' was generated
> ;    By user: swati (1000)
> ;    On host: laptop
> ;    At date: Wed Feb 27 14:16:52 2013
> ;
> ;    This is your topology file
> ;
> ; Include chain topologies
> #include "gromos43a1_lipid.ff/forcefield.itp"
>
> ; Include ligand toplogy
> #include "gromos43a1_lipid.ff/ligand.itp"
>
> ; Include lipid topology
> #include "popc.itp"
>
> ; Include water topology
> #include "gromos43a1_lipid.ff/spc.itp"
>
> ; Include ion topologies
> #include "gromos43a1_lipid.ff/ions.itp"
>
> ; System specifications
> [ system ]
> 128-Lipid POPC Bilayer
>
> [ molecules ]
> ; molecule name nr.
> POPC 128
> SOL 2460
>
> Thanks in advance.
>
> With Regards,
> Swati.
>
>
>
> On Mon, Mar 4, 2013 at 12:45 PM, swati rana <swati.rana088 at gmail.com>
> wrote:
>
> > Dear Justin,
> >
> > Thanks a lot, your suggestions helped me a lot.
> >
> > With Regards,
> > Swati
> >
> >
> > On Sun, Mar 3, 2013 at 1:22 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> >>
> >>
> >> On 3/2/13 1:42 AM, swati rana wrote:
> >>
> >>> Hi Justin,
> >>>
> >>> Thanks a lot, that suggestion of yours helped. I am on the
> >>> equilibration step and its running but nothing is happening on the
> >>> terminal its just stagnant. Is it fine because its more than 17 hrs
> >>> now. Is there some problem.
> >>> After running the second command nothing is happening on the terminal.
> >>>
> >>> grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr
> >>>
> >>> mdrun -deffnm nvt
> >>>
> >>> I am sorry as it is not a reasonable question to ask but i am just
> >>> asking out of curiosity and lack of time.
> >>>
> >>>
> >> If you're trying to run an MD simulation in serial, you'll get
> >> terrible performance unless the system is very small (a few hundred
> >> atoms).  Most MD is conducted in parallel on high-performance
> >> computing clusters, or at the very least on a multi-core workstation,
> again using parallelization.
> >>
> >> You won't get constant output in either case, since I/O is buffered
> >> and write intervals depend on what you specify in the .mdp file.  In
> >> any case, if you're getting poor performance, you're probably simply
> >> asking your computer to do something it's incapable of handling
> efficiently.
> >>
> >>
> >> -Justin
> >>
> >> --
> >> ==============================**==========
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Research Scientist
> >> Department of Biochemistry
> >> Virginia Tech
> >> Blacksburg, VA
> >> jalemkul[at]vt.edu | (540) 231-9080
> >> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www
> >> .bevanlab.biochem.vt.edu/Pages/Personal/justin>
> >>
> >> ==============================**==========
> >> --
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