[AMBER] Changing hydrogen atom radius to optimize saltbridge in GB-OBC model

From: Sunita Patel <sunita.patel.cbs.ac.in>
Date: Sat, 23 May 2020 19:31:04 +0530

Dear Amber-users,

I want to perform a REMD simulation with GB-OBC implicit solvent model. In
the following papers it is mentioned that saltbridges are overstabilized in
GB-OBC model. I want to reduce the GB radius for hydrogen atoms involved in
saltbridges to 1.1 Ang as mentioned in the following papers. I am not clear
where exactly I need to make the changes to satisfy the criteria.

Your help will be highly appreciated.

1) Geney, R.; Layten, M.; Gomperts, R.; Hornak, V.; Simmerling,
C. Investigation of Salt Bridge Stability in a Generalized Born Solvent
Model. J. Chem. Theory Comput. 2006, 2, 115−127.

2) Shang, Y.; Nguyen, H.; Wickstrom, L.; Okur, A.; Simmerling,
C. Improving the Description of Salt Bridge Strength and Geometry
in a Generalized Born Model. J. Mol. Graphics Modell. 2011, 29, 676−

AMBER mailing list
Received on Sat May 23 2020 - 07:00:03 PDT
Custom Search