AMBER Archive (2007)

Subject: Re: AMBER: NAB Average Structure

From: David A. Case (case_at_scripps.edu)
Date: Thu May 17 2007 - 11:32:59 CDT

On Thu, May 17, 2007, adelene_at_stanford.edu wrote:

> Hi, is there a way to use NAB to generate the average coordinates of
> stuctures simulated using MD?

You could save the trajectory (comes out in "binpos" format, I think), and
then use ptraj to compute the structural averages.

Otherwise, the idea behind NAB is that you could modify the code internally.
But remember that you probably want to remove overall translation and rotation
before computing the average structure, so the ptraj route (where all that
stuff is already worked out), may be the way to go.

....dac

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