AMBER Archive (2006)

Subject: AMBER: nmode output with ptraj

From: nadiav_at_soton.ac.uk
Date: Tue Nov 28 2006 - 09:59:02 CST

Dear amber users,

I can see that one can project a trajectory onto pricipal components
calculated within ptraj. I am working with output from Nmode which already
contains the normal modes

Is it possbile to extract the extremes of each eigenvector as a
pdb structure file in ptraj?

I tried to use 'projection' command in ptraj but not got an output and I'm
not sure if it is actually the correct way!

What I want to be able to do is to save individual pdb files of each
eigenvector, preferrably containing the extremes of that eigenvector. I
can use IED in VMD to visualise the eigenvectors but the extent to which
the structure is displaced with respect to the eigenvector is user defined
which I'm not comfortable with.

Thank you in advance.

Nadia

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