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

Smith, Micholas D. smithmd at ornl.gov
Tue Feb 16 14:26:32 CET 2016

At the end of your topology file, make sure you have the correct number of molecules of each type 
(typically the end of the .top file will look something like:

[ molecules ]
Protein    1    ;Number of proteins
SOL        59990 ;Number of waters
Na           2 ; Number of Na ions
Cl            2; Number of Cl ions

In your case you should have something like:

[ molecules ]
Protein       1 ;Number of proteins
MET         (); Number of Methanol Molecules
SOL         (); Number of Solvent molecules

Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Ghada Mhmd <ghada.mhmd22 at gmail.com>
Sent: Tuesday, February 16, 2016 8:19 AM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] error running grompp for ions.mdp input


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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