[gmx-users] Coordinates not matching with topology file

Souparno Adhikary souparnoa91 at gmail.com
Thu Sep 14 10:55:18 CEST 2017

We have generated the *.gro and *.itp file from the ATB server and then did
editconf and solvate. The error that's coming is:

Fatal error:
number of coordinates in coordinate file (g12wt.gro, 33766)
             does not match topology (g12.top, 33698)

If you notice, the error is of 68 atoms. 33766 exactly matches the number
of atoms with the number of atoms of solvent (11200) and the molecule (166)
added. The topology file which we had to write manually was:-

#include "gromos53a6.ff/forcefield.itp"
#include "g12.itp"
#include "gromos53a6.ff/spc.itp"

[ system ]
molecule in water

[ molecules ]
DRG             1
SOL             11200

We are absolutely clueless from where it is computing the 33698 atoms in
the topology file.

We tried adjusting the number of atoms manually but went in vain. Can you
please help us???

Souparno Adhikary,
Department of Microbiology,
University of Calcutta.

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