Hello everyone,
This question is addressed to those that are familiar with MM/GBSA. I have
many protein-ligand complexes and I want to do in batch mode MD and MM/GBSA
with per residue energy decomposition. In that context, it would be much
more convenient to select for each complex the residues that are within R
Angstroms from the ligand to be included in the residue decomposition of
the free energy. Is there any maximum distance Rmax from the ligand (e.g. 6
Angstroms) after which all interactions with the protein residues are
negligible? I can imagine that if the ligand has net charge then the
electrostatic interactions will require higher R value to cancel out.
Thank you in advance for any advice.
Thomas
--
======================================================================
Thomas Evangelidis
Research Specialist
CEITEC - Central European Institute of Technology
Masaryk University
Kamenice 5/A35/1S081,
62500 Brno, Czech Republic
email: tevang.pharm.uoa.gr
tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Sat Mar 11 2017 - 08:00:02 PST
