Dear Daniel,
Thanks for your prompt reply. All I am trying to do is to map different
crystal structures on to top two PCs (principle components), as shown in
Figure 2 of this article
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0040809
Many thanks
Anu
On Thu, Jan 5, 2017 at 4:30 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> It makes no sense to do principal component analysis on a single
> trajectory frame (there is no motion to analyze!). The coordinate
> covariance matrix should be constructed from at least as many frames
> as you have coordinates, otherwise you will have eigenvectors with
> zero eigenvalues. Maybe you wanted to do normal mode analysis? In that
> case you should use the 'nab' program. See the Amber16 manual for
> details.
>
> -Dan
>
> On Thu, Jan 5, 2017 at 11:25 AM, anu chandra <anu80125.gmail.com> wrote:
> > Hello all,
> >
> > I am trying to project the crystal structure of a protein with 210
> > aminoacids, into top two PC (principle component) space. For this, I have
> > carried out PCA of crystal structure with the following script.
> > Unfortunately, all modes came out as zeros. The crystal structure was
> > obtained from PDB. Am I doing anything wrong here?.
> >
> > ------------------------------------------------------------
> ------------------------------------------
> > parm 1atm.pdb
> >
> >
> > trajin 1atm.pdb
> >
> > createcrd crd1
> > run
> >
> > crdaction crd1 matrix covar !.H= name gaccCovar
> >
> > runanalysis diagmatrix gaccCovar vecs 2 name evecs
> >
> > crdaction crd1 projection T1 modes evecs beg 1 end 2 !.H= out T1.dat
> > ------------------------------------------------------------
> -----------------------------------------------
> >
> >
> > Any help would be highly appreciated
> >
> >
> > Many thanks
> > Anu
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
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>
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Received on Tue Jan 10 2017 - 03:00:02 PST
