Hi,
In that case you'll need a set of eigenvectors that you have previously
calculated from e.g. a MD simulation trajectory. Then you would use the
'project' command to project the PDB coords onto those vectors.
-Dan
On Tue, Jan 10, 2017 at 5:50 AM anu chandra <anu80125.gmail.com> wrote:
> 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
>
> > > _______________________________________________
>
> > > AMBER mailing list
>
> > > 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
>
> >
>
> > _______________________________________________
>
> > AMBER mailing list
>
> > AMBER.ambermd.org
>
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> >
>
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>
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Received on Tue Jan 10 2017 - 05:30:02 PST
