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.
--
With regards
Vaibhav A. Dixit
Ph.D.
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X, S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408, +91-7709129400.
E-mail: vaibhavadixit.gmail.com
www.niper.nic.in
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Received on Tue Mar 19 2013 - 05:30:04 PDT
