I am afraid this plugin is not maintained anymore. The archives of VMD
mailing list should be a good source of information regarding this plugin.
Anyway, this is more of a VMD and not Amber list question ..
Best,
Vlad
On 03/19/2013 01:20 PM, Vaibhav Dixit wrote:
> Dear Amber community member,
> On the ambermd.org page the link to the IED
> <http://mccammon.ucsd.edu/ied/>program for analyzing trajectories is
> broken.
> Actually I have performed PCA analysis on my trajectory and wish to
> visualize the normal modes through essential dynamics methodology, but I
> found that no help is available on how to proceed for this. The same link
> given on VMD page is also broken. http://mccammon.ucsd.edu/ied/
>
> Please direct me to the right link so that I can perform IED analysis.
> Thank you.
>
>
> - Visualizing Amber structures and trajectories
> - MOIL-View <http://morita.chem.sunysb.edu/%7Ecarlos/moil-view.html>: an
> Amber and LES-aware molecular graphics package
> - MD Display <http://www.structbio.vanderbilt.edu/%7Ecmoth/mddisplay>, a
> lightweight, Amber-aware trajectory viewer
> - Visual Molecular Dynamics (VMD) <http://www.ks.uiuc.edu/Research/vmd/>,
> another Amber-aware molecular visualization package
> - Chimera <http://www.cgl.ucsf.edu/chimera/>, still another Amber-aware
> molecular visualization package
> - *IED <http://mccammon.ucsd.edu/ied/>, (Interactive Essential Dynamics)
> allows analysis and visualization of essential dynamics
> (akaquasiharmonic) and normal mode results.
> *
> - PCAsuite <http://mmb.pcb.ub.es/software/pcasuite/>, another tool for
> principal component analysis of trajectories.
> - DNA plotting tools <http://www.steletch.org/spip.php?article32>, from
> Stephane Teletchea, shows how to create helicoidal plots from Amber
> trajectories.
>
>
>
--
Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cell and Developmental Biology
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
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Received on Tue Mar 19 2013 - 07:00:03 PDT
