Dear Amber users,
I am running a GBSA MD simulation for a metal-protein that has bound
magnesium ions. I am not sure how to deal with bound magnesium ions with
GBSA. I read Tsui&Case's paper in JPC. B 2001, where they used cobalt
hexammine to model fully hydrated magnesium. However, they did free energy
calculation but not GBSA MD. Because bound magnesium ions in proteins are
not fully hydrated, I think it is not suitable to use cobalt hexammine in
metal-protein cases. Does anybody have experience and ideas to deal with
bound magnesium ions in protein when run GBSA MD simulations?
Thank you!
Wei Chen
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Jul 22 2007 - 06:07:11 PDT
