Re: [AMBER] Failed to calculate entropy with in AMBER14, with no error informations reported in nmode_com.1.out

From: David Case <>
Date: Thu, 9 Feb 2017 09:02:35 -0500

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.


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Received on Thu Feb 09 2017 - 06:30:02 PST
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