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

[swatik at ncbs.res.in]

Dear ALL,

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,


-- 
Swati kaushik
Research Scholar
Prof. R. Sowdhamini's lab
National Center for Biological Sciences
Tata Institute of Fundamental Research
UAS-GKVK campus
Bellary road,
Bangalore- 560065
India
Phone:
 Lab: 0(91)80- 23 66 62 51
      0(91)80- 67 17 62 51
 Fax: 0(91) 80 23 63 66 62
 Email:  swatik at ncbs.res.in
         swati.kaushik15 at gmail.com