AMBER Archive (2003)

Subject: Re: AMBER: average coordinates

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed Nov 12 2003 - 12:24:18 CST

> From owner-amber_at_scripps.edu Wed Nov 12 10:18:44 2003
> Date: Wed, 12 Nov 2003 10:12:20 -0800 (PST)
> From: Bill Ross <ross_at_cgl.ucsf.edu>
> To: amber_at_scripps.edu
> Subject: Re: AMBER: average coordinates
> Sender: owner-amber_at_scripps.edu
> Precedence: bulk
> Reply-To: amber_at_scripps.edu
>
> > Is there a way to make carnal choose only the last
> > 100 steps of the trajectory to perform the averaging?
>
> From the initial example in the manual:
>
> COORD c1 s1 SELECT (1 3 5 200);
>
> This picks sets 1, 3, 5 and 200. As described in the definition
> of COORD SELECT, you can use "SELECT (200-)" to pick all sets
> from 200 onwards.

This would let you create a trajectory with only the desired sets,
which could then be used for a 2nd pass with carnal.

You could also use STREAM WIN to filter the sets you want for a
single pass in carnal. So if there were 1000 sets and you wanted
the last 200:

  STREAM s1 WIN 800 200 my.crd;

Bill Ross

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