[gmx-users] Free energy perturbation of Cu(I) binding

abhigna polavarapu abhignap at gmail.com
Wed Feb 4 04:29:06 CET 2009

Thanks Mark, thats what I really wanted to do. So can you please let
me know where I can find out the way to do position restraints and to
know how these work.


On Tue, Feb 3, 2009 at 10:18 PM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> abhigna polavarapu wrote:
>> Thanks David, But if I just remove the Copper atom and do the
>> simulation as copper is charged there would be sudden change in
>> electrostatics and the protein started unfolding when I ran the
>> simulation for 10ns. So I thought perturbing the charge by little
>> every time I can get a structure with more reasonable than artifacts.
>> Can you please correct me if I am thinking in a wrong way.
> No, you are on the right track, but I think you're trying to apply a tool
> that's not going to fix the underlying problem.
> Metal-binding proteins that are expected to be stable with or without a
> bound metal are likely to undergo some kind of structural change as an
> inevitable consequence of the large change in the electrostatic environment.
> It is simply unreasonable to expect the same point MM charges to be adequate
> for modeling the structure and electrostatics in the two different states.
> If, for some reason, you had sets of charges suitable for the two different
> states, then you simply need to do suitable equilibrations, possibly with
> position restraints initially, until the structures relax.
> However it seems much more reasonable to be doing this with a QM/MM model.
> Mark
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