[gmx-users] error running grompp for ions.mdp input

Ghada Mhmd ghada.mhmd22 at gmail.com
Tue Feb 16 14:19:12 CET 2016


I'm new to gromacs I'm simulating a protein in a mixed solvent
(water/organic solvent)

*first I added my organic solvent molecule (Methanol) using gmx
insert-molecules command

*then I solvate it in water using gmx solvate command

but I went to adding atom using gmx grompp command

*I get this error : Fatal error: number of coordinates in coordinate file
(3im_solv.gro, 161232)              does not match topology (topol.top,
492074) For more information and tips for troubleshooting, please check the
GROMACS website at http://www.gromacs.org/Documentation/Errors
<http://www.gromacs.org/Documentation/Errors> *I don't know which changes I
need to apply on the topology.top file to get it updated
I tried to change the numbers in the .top file to match the number given at
the top of the coordinate 3im_solv.gro file but I still get the same error
but with different numbers.

* any help would be appreciated  *thanks

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