[gmx-users] Re: number of coordinates in coordinate file does not match topology

[Vitaly V. Chaban]

It seems atoms, not molecules... :)

~Vitaly

On Thu, Jul 16, 2009 at 12:36 PM, <swatik at ncbs.res.in> wrote:

> Hi,
>
> thanks for your reply.
>
> Yes their is difference of 5 solvent molecules. They are more in number in
> my topology file.
>
> Regards,
> Swati
>
> >>
> >>
> >> I am running simulation for the drug enzyme complex using Gromacs with
> >> gromacs96(43a2)forcefield. After generating waterbox around my protein,
> >> when I am running grompp command (before energy minimization) I am
> >> getting
> >> following error:
> >>
> >>
> ---------------------------------------------------------------------------
> >> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#
> >> checking input for internal consistency...
> >> calling /lib/cpp...
> >> processing topology...
> >> Generated 380 of the 1326 non-bonded parameter combinations
> >> Excluding 3 bonded neighbours for Protein_A 1
> >> Excluding 2 bonded neighbours for SOL 735
> >> Excluding 3 bonded neighbours for ZPR 1
> >> Excluding 2 bonded neighbours for SOL 36755
> >> NOTE:
> >>  System has non-zero total charge: -1.999999e+01
> >>
> >> processing coordinates...
> >>
> --------------------------------------------------------------------------
> >> Program grompp_mpi, VERSION 3.3.1
> >> Source code file: grompp.c, line: 448
> >>
> >> Fatal error:
> >> number of coordinates in coordinate file (protein_gen.pdb, 119825)
> >>             does not match topology (topology.top, 119830)
> >>
> --------------------------------------------------------------------------
> >>
> >> I checked gromacs wiki page
> >> also(
> >>
> http://oldwiki.gromacs.org/index.php/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology
> >> )
> >> but not able to solve this error.I am getting this error before adding
> >> ions.
> >>
> >> Can anybody help me regarding same and suggest what could be possible
> >> reason for this ?
> >>
> >> Thanks,
> >>
> >> Regards,
> >>
> >
> >
> > I guess you just missed five atoms in your gro file. Does the number of
> > solvent molecules in the coordinate file equal to that in the topology?
> >
> > ~ Vitaly
> >
> >
> > --
> > Vitaly V. Chaban, Ph.D. (ABD)
> > School of Chemistry
> > V.N. Karazin Kharkiv National University
> > Svoboda sq.,4, Kharkiv 61077, Ukraine
> > email: chaban at univer.kharkov.ua,vvchaban at gmail.com
> > skype: vvchaban, mob.: +38-097-8259698
> >
>
>
>
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