Hi Elaine: That you mention was wonderful discovery. Coming closer to my work: What I want to do at the moment is examining if Dock can identify how certain natural products (lipophilic molecules of about 180 first-row atoms) interact with a large protein. I know experimentally that there is interaction, nearly surely with the protein itself and not merely a destruction of the bilayer. Though, I have no idea about the protein region responsible. I have already carried out a conformational search for my natural products by simulated annealing with an algorithm that calls Amber9. Parameter and coordinate files for Amber9 were built with Antechamber. X-ray diffraction data at medium resolution for the protein are available. The tutorials on DOCK does not consider take such a problem (the tutorial starts from a protein-ligand complex elucidated by X-ray diffraction). Professor Brozell suggested that the size of the protein may put a practical limit on the size of Dock's grid, though, one approach would be to divide and conquer the big protein binding sites into subsets that would be processed separately. My question is: can Chimera help such preparation of the protein for docking? Thanks francesco --- Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Francesco, Thanks for your kind words!
Yes, you can view AMBER trajectories in Chimera. Just start "MD Movie" (under Tools... MD/Ensemble Analysis) and in the resulting dialog, there are several choices for trajectory format, including Amber.
The MD Movie tool and input formats are described here: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/ framemovie.html
and are used in this tutorial: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ ensembles2.html
The trajectory input types are not listed in the general "file open" dialog, partly because some formats include more than one file. Also, the more specific MD Movie dialog allows you to specify other parameters, such as the range of frames you want to load. 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 Oct 1, 2007, at 6:22 AM, Francesco Pietra wrote:
Having installed DOCK6.1/DMS (debian Linux parallel amd64) and Chimera 1.2422 (scp-linked desktop Debian Linux i386), may I ask:
1) Can I use Chimera for Amber9 in place of VMD, which I currently use?
2) Being superficially familiar with VMD, I was looking in Chimera for *.prmtop and *.inpcrd file types, as well as rst file, etc.. I suppose I was unable to turn Chimera to use with Amber9.
That said, I was very much impressed by Chimera at the first touch. Thanks francesco pietra
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