Elaine: I had carried out successfully all-by-all pairwise RMSD. Though, it does not help much comparing different ligands for the same protein. As to MMTSB, there are indications about the compilation that I do not understand yet. All in all, it seems to me that a tool for performing affinity analysis for ligands in explicit medium (ideally free energies) is not easily at hand. Hope I am wrong and someone comes with suggestions (I posted the problem of affinities in explicit medium yesterday to DOCK, so a suggestion might come from there too). Thanks francesco --- Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Francesco, The MD Movie tool (which replays trajectories) can also calculate all- by-all pairwise RMSD values and show them as a grayscale map. In the map you can see which frames are similar to which, but the tool does not really perform clustering.
MD Movie (see "RMSD Analysis" section): http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/ framemovie.html
The "Trajectory and Ensemble Analysis" tutorial (part 2) uses this tool and shows an example RMSD map: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ ensembles2.html#part2
Perhaps the AMBER tutorials would be more useful in your situation. I believe tutorial B3 includes clustering: http://amber.scripps.edu/tutorials/
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On Dec 18, 2007, at 6:25 AM, Francesco Pietra wrote:
Is it feasible to command a cluster analysis from rmsd? I would like to group for likeliness snapshots from MD with respect to, say, the structure from which MD was started. Thanks francesco pietra
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