AMBER: PBradii

From: Steve Seibold <>
Date: Tue, 11 Sep 2007 14:40:00 -0400


I have been reading Geney et al from Carlos Simmerling's group about
born radii in AMBER and the "over stabilization" of the salt bridges
when using implicit solvent. I am doing some simulations where I am
"pulling" a ligand from its interior binding site in a protein (crystal
structure) a few angstroms to another site thought to be its entrance
location. I want to use implicit solvent because this is such a large
(gigantic) protein complex. I have applied igb = 5 and mbondi2. However,
I am worried after reading this paper that I should change the born
radii of my hydrogens bound to N-plus atoms from 1.3 to 1.1. The radii
suggested by the paper. Is there a way to do this in AMBER?


Thanks, Steve


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Received on Wed Sep 12 2007 - 06:07:47 PDT
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