[gmx-users] ligand in water

Bratin Kumar Das 177cy500.bratin at nitk.edu.in
Mon May 13 14:45:42 CEST 2019

    The procedure you are following is not ok. Generate the co-ordinate
file of ligand and the topology parameter file. Setup the box and add water
to it. Lastly do energy minimisation.

On Thu 9 May, 2019, 2:33 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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