AMBER Archive (2005)

Subject: AMBER: Mg2+ issues of using MM-PB/GBSA

From: mingche Pan (panmingche_at_yahoo.com)
Date: Thu Dec 01 2005 - 13:01:24 CST

Dear AMBER users,
   
  I wonder whether I can use MM-PB/GBSA method to calculate the binding free energy in the case of Mg2+ directly involving in the ligand binding. The initial tests showed that the energy difference calculated by different GB methods is up to ~80 kcal/mol, and the difference between GB and PB models is also quite large, over 50 kcal/mol. In addition, different Born radii of Mg2+ (from 0.99 ¨C 1.45) also seem giving various energies, ranging from -10 to -130 kcal/mol.
   
  I would appreciate if someone can explain a bit more on this issue, and suggest a method I can use for this situation.
   
  Thanks a lot!
   
  Mingche Pan
   

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