[gmx-users] ligand in water

Dallas Warren dallas.warren at monash.edu
Thu May 9 11:38:34 CEST 2019

This will do it (if need particular water model change with cs switch
options, and assumes ligand.gro has the correct final box size)

gmx solvate - cp ligand.gro -cs -o complex.gro

Unless you have a particular number of waters required, then use.:

gmx solvate - cp ligand.gro -cs -o complex.gro -maxsol ####

To both above add -p topol.top if want it to automatically update the
topology file with number of molecules/residues. Otherwise you need to do
by hand, which is easy enough.

Or even if need a particular water coordinate file:

gmx insert-molecules -f ligand.gro -ci water.gro -nmol #### -o complex.gro

On Thu, 9 May 2019, 7:02 pm RAHUL SURESH, <drrahulsuresh at gmail.com> wrote:

> Hi Users.
> I want to simulate ligand in the water box. I prepared a water molecule and
> started with pdb2gmx and then planned to follow protein-ligand tutorial.
> Unfortunately ended up with an error in gro file format. Have check every
> possibility but still couldn't find any solution.
> My initial pdb is water.pdb and the corresponding gro file is water.gro. I
> clubbed the ligand gro file and water gro file as complex.gro. I have
> uploaded the file here. can anyone help me with the format issues>?
> --
> *Regards,*
> *Rahul *
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