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

[Ghada Mhmd]

I'm still getting the same error but with different numbers even though I
calculated the number of molecules of each [Moleculetype] in the .gro file
and changed the number accordingly

On Tue, Feb 16, 2016 at 4:26 PM, Smith, Micholas D. <smithmd at ornl.gov>
wrote:

> 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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