AMBER Archive (2006)

Subject: AMBER: ions+proteins

From: Hannes Loeffler (hal_at_iam.u-tokyo.ac.jp)
Date: Mon Jun 19 2006 - 20:45:57 CDT

Dear list members,

I have a somewhat general question to the simulation community and hope
not to be too offtopic (but if anybody points to other useful
information resources besides CCL I would be grateful too).

I am interested in the "quality" of counterion model for typical ions
such as Na+ or Cl- used as counterions in protein simulations. Are
there any studies trying to assess the validity of the simple
Lennard-Jones+point charge for various phyisco-chemical properties,
e.g. the effect on the stability of proteins, etc.? What about
residence times or structural changes induced by ions? Are there
detailled comparisons with this model and, say, models that try to
incorporate polarization explicitly?

I am grateful for any answers,
Hannes.
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu