AMBER Archive (2007)

Subject: AMBER: PBradii

From: Steve Seibold (seibold_at_chemistry.msu.edu)
Date: Tue Sep 11 2007 - 13:40:00 CDT

Hi AMBER

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

 

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