AMBER Archive (2009)

Subject: [AMBER] MMGBSA IG Value

From: Rajesh Raju (Rajesh.Raju_at_postgrad.manchester.ac.uk)
Date: Fri Mar 20 2009 - 12:20:52 CDT

Hi,

I want to do MMGBSA free enrgy decomposition and binding energy
calculations for my protein-ligand system. Which IG option (IG=1, 2, 5
) should i use ? Can i use the same paramter file for IG=1 and IG =2 .

I read somewhere inorder to use IG =2 I should use the leap command

''set default PBradii bondi'' when setting up the prmtop file? But I
have dount that I am doing MMGBSA (not PBSA). So should I modify the
prmtop file?

Cheers

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