AMBER Archive (2004)

Subject: AMBER: ions in mm_pbsa

From: Fang, Jianwen (
Date: Thu May 06 2004 - 10:30:12 CDT

        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,

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