On 6/10/2011 3:52 PM, shahid nayeem wrote:
Dear All
I want to refine a protein homology model, I did minimization but then
procheck does not give better Ramachandran plot.
EM can only do a local minimization, and there is no good reason why
that should show a marked improvement on an arbitrary homology model.
This model is a homodimer with each chain of 609 residue and a total
of 1218 residue so a long MD simulation to search native state is not
feasible. Can any one help me on this list to tell that how should I
attempt this problem.
Short MD will also be unlikely to do anything useful, because it is
strongly determined by the initial conditions. So GROMACS is unlikely to
be the tool you need for this problem, nor this list the place to find
it. I would consult the homology modelling literature and software tools.
Mark
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