[AMBER] Magnesium ion and MMPBSA/GBSA

From: Francesco Gentile <fgentile.ualberta.ca>
Date: Mon, 12 Dec 2016 00:44:04 -0700

I am running free energy calculations on a series of protein-ligand
complexes. The ligands are all interacting with a magnesium ion in the
active site of the enzyme. How should I treat the magnesium ion (part of
the receptor, the ligand or what else?)? Also, does someone has experience
with this kind of situation and maybe can help me in setting up correctly
the calculation? Thanks in advance

Francesco Gentile
PhD Student, Biophysics
CCIS 3-215, Department of Physics
7-112, Li Ka Shing Centre for Health Research Innovation
University of Alberta, Edmonton, AB T6G 2E1
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Received on Mon Dec 12 2016 - 00:00:02 PST
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