AMBER Archive (2006)

Subject: Re: AMBER: nmode output with ptraj

From: David A. Case (case_at_scripps.edu)
Date: Tue Nov 28 2006 - 20:36:33 CST

On Tue, Nov 28, 2006, nadiav_at_soton.ac.uk wrote:
>
>
> Is it possbile to extract the extremes of each eigenvector as a
> pdb structure file in ptraj?
>
> 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.

I'm not sure what you mean by "the extremes of each eigenvector", or how such
an idea is not always "user defined". I'm pretty sure you can't do what you
propose inside ptraj, and IED seems like a natural place to start from. I
guess the best course depends a lot on what you want to do with pdb files once
you have them....

...regards...dac

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