I want to solvate a ligand molecule with (united-atom) octanol. I have a pre-equilibrated box of 512 (united-atom) octanol molecules. I am using editconf and genbox tool for solvating the ligand molecule:
'editconf -f ligand.gro -c -d 1.0 -bt dodecahedron -o box.gro'
'genbox -cp box.gro -cs octanol_512.gro -o solvated_box.gro'
It seems that genbox is not doing it properly - the molecules are not closely packed; there could have been more octanol molecules inside the box. Is there any other way to solvate a ligand molecule with a non-aqueous solvent?
I have had good success using packmol to build solvent boxes for use with Gromacs -- it's worth a look: https://code.google.com/p/packmol/
The problem might be that due to collisions the algorithm was not able to place more. Simply start with a much bigger box and equilibrate your system, which you have to do anyway, in an NPT ensemble.
You could first generate a box of equilibrated octanol (which you already seem to have), and place your solute in the center of box, and remove all the octanol molecules with some cut-off distance (3A?) to the solute atoms. This will avoid steric overlap and ensure smooth equilibration later on. After removing the colliding octanol molecules, change the number of octanol molecules in your topology file.
Thanks for your reply. Thus I can use editconf to place the solute at the center of the box. Now is there any options in editconf or genbox such that I can set the cut-off distance to the solute say 3A?
I am not sure if there is any readily available script for removing overlapping molecules. It should be quite straightforward to write a perl/python script to identify all the octanol molecules overlapping with the solute and get the molecule indices. Once you have the indices, you can just remove them from the .gro file, and also change the count in the topology file.
I have had good success using packmol to build solvent boxes for use with Gromacs -- it's worth a look: https://code.google.com/p/packmol/
As Vincent mentioned, packmol would be my tool of choice for this. One can accomplish a similar result using VMD, although in my option it would take more effort.
hi. please guide me.i want solvate a protein in ethanol but i dont know how we can do it? i dont know , how can i produce a ethanol box? And what changes should I make in top file after solvation?
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