[gmx-users] Request on help in ED method
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:
> 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...
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
More information about the gromacs.org_gmx-users