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

[Vitaly V. Chaban]

By hand is the easiest way.


>
>
> Ya, sorry I wrote it wrong.But why these extra atoms are present in my
> topology file and how to correct it.
>
> Thanks,
>
> Regards,
> Swati
>
> >
> > 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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