AMBER Archive (2004)

Subject: Re: AMBER: reference with ptraj

From: Bill Ross (
Date: Thu May 06 2004 - 17:05:55 CDT

> ... to get the RMSd
> to the average structure is has to be done in two runs, the first to
> generate the average structure
> trajin annealing.traj 175 200
> average average.pdb pdb

Does 'average' automatically rms fit each frame to the 1st?

Normally one would want to fit to the 1st frame before adding
coordinates to avoid drift and rotation artifacts. Once an
average structure is obtained, it is worth visualizing it
to check for artifacts of internal motions, and then energy
minimizing it in order to get reasonable bond lengths etc.

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