AMBER Archive (2006)
Subject: AMBER: Simulating proteins with calcium ion
From: Qing Zhang (qingzhang_nyu_at_yahoo.com)
Dear Amber users:
I am trying to simulate a protein-protein complex with a calcium ion (Ca2+) at the binding interface. Energy minimizations on the initial crystal structure without explicit solvent lead to displacement of Ca2+, even though the ion is restrained. I searched the Amber achieve and found that the similar problems had been raised before and that two kinds of models had been used for solving the problem: bonded and non-bonded. The latter is preferred in my case because an experiment shows that the mutation of a particular residue that bonds to Ca2+ leads to partial dissociation of the complex.
Although there have been clear demonstrations of non-bonded models for Zn2+ with Amber and Ca2+ with Charmm (indicating divalent ion coordination after MD simulations), I did not see such a clear demonstration of a nonbonded model for Ca2+ with Amber. Anyone knows?