AMBER Archive (2002)

Subject: non-bonded metal ion in complex

From: yuann (yuann_at_bioinfo.ndhu.edu.tw)
Date: Tue Sep 17 2002 - 01:28:45 CDT

Greetings all,
  I now get trouble with dealing with a non-bonded metal ion in a complex
before running sander. This complex forms with two identical organic
molecules and a magnesium ion which is near two O(-). (R-O- [Mg2+] -O-R)
Initial structure was taken from PDB. I'm worried that magnesium ion will
act as a free ion during energy minimization/MD due to no suitable
parameter for this condition. Can I solve this problem by applying a
harmonic restrain with force constant(eg. 100K ) or edit prmtop file of
this molecule to become a residue instead of three residues? (I remember
this skill is mentioned in DNA Tutorial, but have no idea what to do in
this case.)
  Any comment will be appreciated.

Best Regards,
sychen.