AMBER Archive (2004)

Subject: FW: AMBER: ions in mm_pbsa

From: S. Frank Yan (SYan_at_gnf.org)
Date: Thu May 06 2004 - 12:23:55 CDT


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_at_ku.edu]
        Sent: Thu 5/6/2004 8:30 AM
        To: amber_at_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

         

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu