AMBER Archive (2004)

Subject: Re: AMBER: question about the average structure from ptraj

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Sun Feb 08 2004 - 13:47:11 CST

> I used ptraj to generate average structure for my simulation. I noticed
> the orientation sidechain of one residue was distorted a lot compared with
> initial input structure. However, when I viewed my trajectory file using
> VMD, the sidechain of that residue was in the same orientation as in the
> input file. Anyone has many clues here about what might be the problem?
>
> ptrajin file is here
> ptraj AR.top << EOF
> trajin AR.md.crd
> average AR.agonist.average.pdb start 1 stop 200 offset 1 pdb nowrap nobox
> EOF

You should probably RMS fit when averaging, to align the frames of the
trajectory. Another factor affecting averaging is if say a sidechain
moves between configurations, which can result in even an impossible
config for the average. It doesn't sound like this is the case here,
but one should bear the possibility in mind when averages go wrong.

Bill

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