Re: AMBER: NAB Average Structure

From: Andreas Svrcek-Seiler <>
Date: Thu, 17 May 2007 21:40:26 +0200 (CEST)

On Thu, 17 May 2007, adelene.Stanford.EDU wrote:

> Thank you. Is there "ptraj" feature in NAB? I don't see that in the manual.
> I was thinking more in terms of combining different pdb output files which I
> obtained from MD in NAB - is there a way of averaging out the structures? I'm
> also concerned if this will cause unphysical bond angles and lengths, so any
> advice is welcome.
With nab comes the "suppose" program, which can not superimpose
structures, but also calculate an average(d) structure. The
superposition is not mass weighted (I never checked systematically how
strongly this affects the results for peptides or RNA/DNA).

"suppose start.pdb snapshot*.pdb -mean"
would superimpose all snapshots to the structure in "start.pdb",
calculate an averaged structure and store that in "mean.pdb".
As for unphysical bond angles etc.: you have to live with them
or minimize the averaged structure to get a minimized averaged structure.
For testing purposes, I'd suggest a nucleic acid helix.
Unless any base pairs open and/or close averaged structures look very good
here (I like to use them for demonstration purposes).

good luck

P.S.: I'v written everything from memory, so please forgive any

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Received on Sun May 20 2007 - 06:07:26 PDT
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