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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--
-------------------------
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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Received on Thu Jan 05 2017 - 09:00:02 PST
