AMBER Archive (2006)

Subject: AMBER: Zn2+ and Ca2+ ions explicitly treated in MMPB/GB/SA

From: Piotr Cieplak (cieplak_at_cgl.ucsf.edu)
Date: Mon Dec 04 2006 - 18:20:02 CST

Dear All
I am having problems with setting mm/pb/gb/sa calculations
for metalloprotease that includes 2xZn2+ and 3xCa2+.
Does anyone have any experience what radius should I use for Zn2+ and Ca2+
in mm/pbsa calc?
As I understand I need to add those radii to the mm_pbsa_calceneent.pm file.
Am I right?

Thanks for any help
Piotr
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