[gmx-users] Request on help in ED method

David spoel at xray.bmc.uu.se
Fri Dec 27 10:16:35 CET 2002

On Fri, 2002-12-27 at 11:10, Dmitry Egorov wrote:
> From

>   Third. Most main question - may I and if yes, how may I obtain end
> conformations of my original structure projected on eigenvectors and is it
> possible to obtain these conformations with the all ( not only C-alpha atoms
> that was used in g_covar for analysis ) atoms.
> Thank you very much for your attention to my problem.
Dmitry, that was a very long mail. Too long for me to read entirely. For
background I suggest you look up the Garcia paper in Phys Rev Lett
  author =       "A. E. Garcia",
  title =        "Large-Amplitude Nonlinear Motions in Proteins",
  journal =      BTprl,
  year =         "1992",
  volume =       "68",
  pages =        "2696--2699",
this gives very good background.

You should be able to reproduce most analysis described in the Berendsen
group's papers, but the answer to  your final question is: not directly.
You will obtain coordinates of C-alpha only. You can fit the average
structure or reference structure on each of the C-alpha conformations
using g_confrms, but that seems not to be correct...

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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