[gmx-users] Binding Copper to Protein
Justin A. Lemkul
jalemkul at vt.edu
Sat Mar 21 13:05:37 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?
If you are ever asking yourself, "Can I take part of one force field and
introduce it into another?" the answer is always *absolutely not.*
However, CU2+ is part of OPLS (in ions.itp, there is CU2+ after #ifdef
_FF_OPLS), and a reference for these parameters is given in ffoplsaa.atp.
> 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?
You can try it and see. Whether or not you think it's appropriate is going to
depend on what is known about your particular system. But if you are defining a
bonded interaction of any sort between a metal ion and an amino acid side chain,
I would argue that the original HIS topology is no longer valid, since it is
sharing electrons with the metal, thus affecting the charge of all species
involved in the bonded interaction.
> Thanks. I appreciate your time.
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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