On Thu, Feb 09, 2017, wei wrote:
> Dear all, I want to calculate entropy contribution of a relatively
> huge protein (18574 atoms) binding with it's ligand.
Just storing the second derivative matrix would require 24 Gb of memory;
the nmode program might need twice this much.
A better strategy (in my view): cut the protein down to a region just
around the ligand-binding site, and estimate the entropy change +/-
ligand from that. You will be missing some long-range effects, but it
is an open question whether those effects (assuming you *could* calculate
them) would be accurate in any case.
...dac
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Received on Thu Feb 09 2017 - 06:30:02 PST
