Thanks for the suggestions Daniel.
On Tue, Jan 10, 2017 at 1:03 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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
> >
> > > > _______________________________________________
> >
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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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> >
> > > AMBER.ambermd.org
> >
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> >
> > >
> >
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> >
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> >
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> >
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> >
> >
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Received on Thu Jan 12 2017 - 05:30:03 PST
