You don't need to keep the neutralizing ions of the system in MM-PBSA
calculations. PB model asks you to specify a ionic strength in the
electrostatic solvation free energy calculation, but it usually has
little effects on the final results. Frank
-----Original Message-----
From: Fang, Jianwen [mailto:jwfang.ku.edu]
Sent: Thu 5/6/2004 8:30 AM
To: amber.scripps.edu
Cc:
Subject: AMBER: ions in mm_pbsa
Dear all,
I am using mm_pbsa to calculate protein-ligand affinity.
I used 16 Na+ to neutralize the system. My question is: should I keep
ions when I generate complex snapshots? Is the implicit solvent model
smart enough to neutralize the charge?
Thanks in advance,
JF
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Received on Thu May 06 2004 - 18:53:01 PDT
