[gmx-users] Analyzing Protein-Ligand Interactions

[Nancy]

Hello All,

I am trying to analyze the output of repeated molecular docking runs, so
that I further refine the protein-ligand complex using GROMACS, and
determine the free energy of the system.  Is there a program that can
process a number of ligand structure files (output of docking runs) as
input, determine protein-ligand interactions, list them, and visualize
docked conformations?

If anyone has information, I would greatly appreciate it.

Thanks in advance,

Nancy
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