[gmx-users] Dihedral angle PCA

David van der Spoel spoel at xray.bmc.uu.se
Thu Apr 11 17:35:18 CEST 2013

On 2013-04-10 08:33, anu chandra wrote:
> Dear Gromacs users,
> I would like to do side-chain dihedral angle PCA for my protein. The
> protein contains 293 residues. I came across an explanation about dihedral
> PCA in gromcas website (
> http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA). Is it possible
> to do side-chain dihedral PCA using the same methodology? Is there any
> other programmes anyone came across for side-chain dihedral PCA?
> Waiting for your valuable reply.
> Thanks in advance
> Regards
> Anu
Have you tried following the steps there? I think it should work.

Other than that dihedral PCA is regarded as not very useful by at least 
some people because it is difficult to interpret the results in 
structural terms. For instance maxima in a multidimensional torsional 
energy landscape may be due to atoms coming close (hence preventing the 
sampling) without giving any real information on the structures. But 
this is for you to decide :).

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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