[gmx-users] Dihedral energy map along two eigenvectors to actual conformations

[Justin A. Lemkul]

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
> 

-- 
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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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