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

[Smith, Micholas D.]

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

hello

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
Ghada
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