[gmx-users] Binding Copper to Protein
genesup at gmail.com
Sat Mar 21 12:08:36 CET 2009
I am working with enzyme that contains Cu2+ in the active site. During a
free simulation it always gets out due to minor conformational changes
of coordinating residues. Since the copper is known to be essential for
enzyme catalysis I want to set some extra force to bind it to certain
1/ I have not found CU2+ in opls ff. In ions.itp CU is defined as CU2+
atomtype which I think is taken from GMX ff. Is it correct to use GMX
Copper parametrization with OPLS?
2/ What is the easiest way to bind a metal ion to a histidine residue?
What if I add the bond to specbonds.dat without changing HIS topology
(dihedral can be set to 0 0 0 0 0 0 in the itp file of the protein)? Can
this be correct?
Thanks. I appreciate your time.
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