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

Polavarapu, Abhigna polavara at indiana.edu
Tue Feb 3 22:55:03 CET 2009

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.

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