AMBER Archive (2005)

Subject: AMBER: questions about MG ions

From: JIANING WANG (wangj_at_uga.edu)
Date: Sun Jul 31 2005 - 18:12:36 CDT

Hi, all,

I have an pdb structure with Mg ion bound to two deprotonated Asp residues
and nucleotide triphosphates. However, when I performed the minimization in
Amber, Mg ions moved away from the original place. I saw some people
suggestted using some distance constraints to the metal ions, but in my sense,
if metal ions coordinate with some residues, it should not move even without
constraint. Does anybody have such experience? How to deal with metal ions?
Thanks in advance!
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