AMBER Archive (2002)

Subject: Polarizabilities, charge scaling and ions

From: Michal Otyepka (otyepka_at_aix.upol.cz)
Date: Wed Mar 27 2002 - 03:42:29 CST

Dear AMBER users,

there is Br- ion in the active site of our system. We are searching for a
way how to treat such ion or ions in an active site generally. The first
idea is to use polarizability for Br- ion only but required parameters are
not present in the parm98.dat force field. It evokes two questions 1, how
to develop parameters, and 2, can one use polarizability only for 1 res
(and does exist anywhere any example)? The other one idea is to scale
charges because an effective Br- charge is not -1. It evokes some
questions 1, can one scale charge only for 1 res or can one use charge
e.g. -0.80 for such ion, 2, has one to scale charges for complete protein,
3, does exist any tests or articles comparing polarizabilities/charge
scaling etc. 4, could somebody recommend me some articles in the field?

      
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