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

David Mobley dmobley at gmail.com
Wed Feb 4 00:13:34 CET 2009

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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