AMBER Archive (2009)

Subject: Re: [AMBER] re: essential dynamics

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Wed May 13 2009 - 12:48:42 CDT

On Wed, May 13, 2009, Chunliyan wrote:
>
> My protein looks like this. I do know my trajectory is normal. I use
> IED to open .ppj, .ppv and topol.pdb file.

Does it look OK if you set all eigenvector amplitudes to zero? Then you
should see the same thing as a "regular" VMD picture, where you load the
prmtop file and a coordinate file.

This may not be something that is readily debugged via email.

...dac

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