[gmx-users] error coordinates in .gro donnot match .top

Asmaa Elsheshiny pyaaea at leeds.ac.uk
Mon Oct 5 11:43:17 CEST 2009

Hi, all
when I want to use gromacs preprocessor grompp to obtain  .tpr to use in the energy minimization as follow
 grompp -f minim.mdp -c bradywaterbox.gro -p brady.top -o minimbrady.tpr

I got the following error message
Fatal error:
number of coordinates in coordinate file (bradywaterbox.gro, 670)
             does not match topology (brady.top, 0)

where,  bradywaterbox.gro & brady.top are obtained from 
genbox -cp solvatedbrady.gro -cs spc216.gro -o bradywaterbox.gro -p brady.top

I think that the topology file didnot include the solvent molecules so it canont be mached with the coordinate file .gro , did it?
So how can I fix this problem?


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