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

[abhigna polavarapu]

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.
abhigna

On Tue, Feb 3, 2009 at 6:13 PM, David Mobley <dmobley at gmail.com> wrote:
> Perhaps this is obvious, but typically you only want to do free energy
> perturbation if you are interested in computing a free energy
> difference. If you are merely interested in structural properties of a
> different system (in this case, the protein without the copper there)
> you can simply make the change to the system (here, remove the copper
> atom) and run long enough for it to reach equilibrium.
>
> On Tue, Feb 3, 2009 at 3:55 PM, Polavarapu, Abhigna
> <polavara at indiana.edu> wrote:
>> Hi all,
>>        Thank you for the help till now and I successfully generated the forcefield Cu(I) binding protein. Now I wanted get the structure of non-copper bound form which I think I can do by perturbing the charge on Cu(I) and even perturbing the bonded and nonbonded parameters. Is there a way I can do this with Gromacs and when I read through chapter five I could understand the way it is done but I am not really confident about the protocol of getting the good structure for nonbonded protein with Cu(I). Can any one tell does this method works for this kind of situation where I have a Copper bound protein and by perturbing its bonded and nonbonding interactions one could arrive at the nonbonded protein structure and the energy difference. Thanks in advance.
>> abhigna
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