[gmx-users] MMPBSA - with water molecules in the binding site

[Gabriela Aucar]

Dear gromacs users,

I have 100ns of production run of a Protein-Ligand Complex, and I want to
perform an MMPBSA calculation including water molecules of the binding
site. Can I do that with g_mmbpsa tool ? I tried to obtain a new trajectory
with the water molecules of the binding site, and the protein and ligand
with VMD but I didn't succeed.

Any help will be apprecieated

Thanks in advance,

M. Gabriela