On Thu, Oct 15, 2020, SATYAJIT KHATUA wrote:
>
>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?
I'm a little confused: is the water one of the four ligands for the
"tetra-coordinated" zinc?
Basically, if a water is "sructured" (likely to stay in one place),
you should retain it, i.e. treat it as part of the protein, not part of
the solvent.
...dac
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Received on Thu Oct 15 2020 - 11:30:02 PDT
