Ali Naqvi wrote:
Hi all,
I have been following the method outlined by Yuguang Mu to generate the
energy landscape along two eigenvectors. There are four minima that I
wish to explore. I can determine the points along the vectors that
correspond to the conformation, but am unsure of how to use those to
obtain the corresponding pdb as was shown in the paper:
Mu, et al. Energy Landscape of a Small Peptide Revealed by
Dihedral Angle Principal Component Analysis, 2005.
Any insight?
Have you tried the dihedral PCA how-to? I don't know if it will give you
everything you want, but it's certainly a start.
http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA
-Justin
Cordially,
Ali
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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