Re: coordination chemistry with NAMD

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Fri Aug 04 2006 - 10:50:30 CDT

Hi Gaurav and Jan,

Since I was the one who suggested this "virtual bond", I have to
apologize for skipping this detail. Jan is right, you could obtain
such a "crooked" geometry. I think that the optimization of the vdW
radii will not be as painful as the full parametrization.

Sam, thank you for this comment!

Michel

2006/8/4, Jan Saam <saam_at_charite.de>:
> Hi Gaurav,
>
> when you are modelling the coordination bonds using nonbonded
> interactions you'll most likely end up with a crooked geometry of the
> complex because the VDW radii are not optimized for the interaction of
> two adjacent ligands. But if you know the complex geometry, e.g.
> tetrahedral or octahedral you can adjust these parameters accordingly.
>
> Jan
>
> Gaurav Sharma wrote:
> > Hi Meredith, Nitin, Michel and others,
> >
> > Thanks for your response, they have been all very insightful. So it
> > seems there are two possible ways to simulate metal ion - protein
> > interactions:
> >
> > 1. By artificially creating a bond between the cation and the nitrogen
> > atom of His residue and updating the force-field with the new
> > parameters for the bond.
> >
> > 2. By treating the coordination bond as a non-bonded interaction and
> > simulating it with the already available parameters in the charmm ff.
> >
> > My goal is to study the conformational changes induced by divalent
> > ions in proteins. So I guess the best procedure for me would be to
> > place the metal ion near the His residues and simulate the system
> > assuming that the non-bonded interactions are sufficient to simulate
> > the dynamics involved. I hope this is a simple and effective way to
> > solve my problem. Please let me know of your thoughts for the same.
> >
> > Also does anyone know of similar parameters for divalent ions other
> > then Zn (such as Ni+2, Cu+2 etc.)
> >
> > Thanks again for your help.
> >
> > Gaurav
> >
> >
> > Meredith Foley wrote:
> >
> >> Hi Gaurav-
> >>
> >> There's a paper out describing the representation of divalent ions,
> >> particularly Zn+2, in the charmm force field. To guarantee accurrate
> >> bond lengths, you'd have to do qm calculations, but depending on the
> >> data you're hoping to generate, the charmm force field may be good
> >> enough.
> >>
> >> This is the paper:
> >>
> >> R. H. Stote and M. Karplus. 1995. Zinc Binding in Proteins and
> >> Solution: A Simple but Accurate Nonbonded Representation.
> >> Proteins23:12-31.
> >>
> >> Best of luck,
> >>
> >> Meredith
> >>
> >> On 8/2/06, Gaurav Sharma <sharma_at_coe.neu.edu> wrote:
> >>
> >>> Hi All,
> >>>
> >>> I want to simulate Zinc ion - Histidine coordination bonding using
> >>> NAMD.
> >>> Is it possible to simuate this bond with the available parameters for
> >>> Zn+2 ion in the Charmm force-field?
> >>>
> >>> Can this bond be modeled as a covalent bond with some tweaking of the
> >>> parameters?
> >>>
> >>> A more generic question would be: Is it possible to simulate
> >>> coordination bonds between metal ions and protein?
> >>>
> >>> Thanks for your help.
> >>> Gaurav
> >>>
> >>>
> >>>
> >
> >
>
> --
> ---------------------------
> Jan Saam
> Institute of Biochemistry
> Charite Berlin
> Monbijoustr. 2
> 10117 Berlin
> Germany
>
> +49 30 450-528-446
> saam_at_charite.de
>
>

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