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

[Vitaly V. Chaban]

>
>
> 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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