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

swatik at ncbs.res.in swatik at ncbs.res.in
Thu Jul 16 08:37:20 CEST 2009

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
  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
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 ?



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
 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

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