[gmx-users] force field Parameters for DPG
Mark.Abraham at anu.edu.au
Mon Oct 12 14:04:56 CEST 2009
Olaniyi Yusuff wrote:
> I am using molecular dynamics simulation to monitor the conformational
> transition of human adult hemoglobin from the deoxy- to the oxy-state
> and the effect of 2,3-DPG on the binding of oxygen to the hemoglobin
> molecule using gromos force field G43a1 in gromacs.
> Please i want to know if any one have the force field parameters the DPG
> or how to about the parametrisation. The formula for DPG is C3H4O10P2
Don't pre-suppose the force field. You will wish to see what MD
simulations have been done on organophosphates and/or hemoglobin under
what forcefields with what simulation packages, etc. That should guide
your choice of methodology. Be aware that classical MD is unlikely to be
suitable for modelling the kind of charge-transfer interactions that
occur when p-block atoms complex transition metals, so you're unlikely
to be able to study the actual transition. If you wanted that, you might
need QM/MM techniques even after you've parameterized 2,3-DPG.
Parameterization itself is an expert topic - see
for the standard advice.
All things considered, I might expect a post-doc with solid MD
experience to spend most of a year getting anywhere such a project :-)
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