Dear Users,
I am using MMPBSA.py for the first time to calculate the binding free
energy for my ligand bound enzyme system. After consulting manuals and
tutorials, I came to know that essentially I require four topology files:
one for the entire complex, one each for the receptor and ligand as well as
a solvated topology file for the complex as I have planned to execute MD
runs in explicit water. My enzyme system contains a tetra-coordinated zinc
ion at the active site and one of the sites is occupied by a crystal water
molecule (as ligand is not directly bonded to the metal center but in a
pocket near the active site). My question is whether I have to strip that
crystal water of from the pdb during complex topology formation or should I
retain it?
Thanks a lot,
Satyajit Khatua
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Received on Thu Oct 15 2020 - 10:00:02 PDT
