[gmx-users] genebox and solvate command

Justin Lemkul jalemkul at vt.edu
Mon Feb 15 16:00:26 CET 2016

On 2/15/16 2:07 AM, Mehreen Jan wrote:
>   when I have run the genbox command, it has shown that "This tool has been removed from Gromacs
> 5.0. Please see
> http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0
> for ideas how to perform the same tasks with the new tools."
> In gromacs site, it is written that
> genbox
> This tool has been split to gmx solvate and gmx insert-molecules.
> gmx
> for solvate command:
> solvate -cp *.pdb -cs spc216.gro -p topol.top -o *.pdb
>   error:
> undefined solute box
> create one with gmx editconf or give expicit -box command line option??
> what about gene box???
> with "gmx help solvate"  and "gmx help
> insert-molecules it is not clear what should i do???
> what command are used???

The error message tells you exactly what to do:

"create one with gmx editconf or give expicit -box command line option"

You're trying to solvate a system that does not have a defined size, so clearly 
that fails.  Do some basic tutorials and you will see what to do.  "gmx solvate" 
is basically identical to "genbox" in this regard.  Since 5.0, the only thing 
that has changed is that the ability to insert molecules into the box has been 
split off into a separate tool.  Otherwise "gmx solvate" and "genbox" are 
actually identical for all practical purposes.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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