Hi
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, wrote:
> Hi Users.
>
> I want to simulate ligand in the water box
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 -
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
