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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