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?
*---------------------------------------------[*]-*
| Department of Inorganic and Physical Chemistry |
| Palacky University |
| tr. Svobody 26, 771 46 Olomouc, Czech Republic |
| |
|ph. +420 68 563 4756 fax +420 68 522 5737|
| fax +420 68 563 4420|
|
http://aix.upol.cz/~otyepka |
|
http://www.upol.cz/kafch |
*-------------------------------------------------*
Received on Wed Mar 27 2002 - 01:42:29 PST
