[AMBER] how to retain the MG++ coordination geometry during simulation

From: BERGY <nucleic81.gmail.com>
Date: Tue, 2 Dec 2014 12:59:57 -0700

Hi amber -users,

I have a protein crystal structure with ATP in the ligand site and a
coordination bond with 6 oxygen atoms. i.e. three from water oygen, OH
from Serine, two oxygens from ATP. They all are within 2.1 Angstroms from
the Ion. The question is, while carrying out the simulation, Is it
necessary to have some distance or angle or dihedral restraints to maintain
the coordination bonds.

Best,
Bergy
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Dec 02 2014 - 12:30:02 PST
Custom Search