[gmx-users] force field Parameters for DPG

[Mark Abraham]

Olaniyi Yusuff wrote:
> Hello,
> 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 
http://www.gromacs.org/index.php?title=Documentation/How-tos/Parameterization 
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 :-)

Mark