Dear Users,
I am working on some ligand-bound metalloprotein systems. Following the
tutorials and manuals from ambermd site, I understood that system
preparation is a very important step here. Although there is a hint on how
MMPBSA.py can be used for the case of the ligand-protein complex in manual,
I am wondering how can I implement this into my systems as they contain a
catalytically important metal center at its active site (I think there is
no tutorial about the system preparation of a ligand-bound metalloprotein).
It is very straight forward in the case of the complex. For the ligand, it
is also not very hard to prepare the topologies. This leaves us only to the
parameterization of the protein system. Now as the metal center is
important, I can't just strip it off from the protein, right? And another
thing if there is any crystal water connected to that metal center to
fulfill its coordination number, should I have to retain it for the case of
protein parameterization (talking about protein only, not the complex)?
with regards,
Satyajit Khatua
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Received on Mon Oct 26 2020 - 21:30:02 PDT
