AMBER Archive (2003)

Subject: Question: Nmode with counter ions.

From: Masaki Tomimoto (masaki_at_stromix.com)
Date: Thu Apr 24 2003 - 12:09:02 CDT

Hi All,

I am going to perform N-mode a protein (~ 250 a.a.) which contains Mg2+ inside the protein (it is seen X-ray crystallographically), and is given two Cl- for electrostatic neutralization by leap. My question is, (1) shall we keep both ions in N-mode, (2) shall we keep only Mg2+ in N-mode, (3) shall we ignore all ions, (4) other suggestion.

Thanks,

Masaki Tomimoto
Sr. Scientist, SGX Inc.