Hi Daniel and David
Thanks for replies.
1) >> The last 'projection' command will create 3 data sets (corresponding
to projections for PCs 1, 2, and 3)
Sorry I meant the plots of, say, PC1 vs PC2 etc. which I can obtain with
"projection modes evecs.dat out myproj.txt beg 1 end 3 :1-328.N"
But am not able to get plot for Eigenvector vs Displacement (residues/atoms
displacement along eigenvectors) and I get this error always:
Error: Modes should be read in prior to this command with 'readdata'
This seems to be simple to resolve, here is the commands sequence: (I tried
using 'modes' after and before readdata its not working)
crdaction crd1 rms ref [avg] :1-328.N
crdaction crd1 matrix covar :1-328.N name myCovar
runanalysis diagmatrix myCovar out evecs.dat vecs 15
readdata evecs.dat
modes displ out dis.dat name myCovar beg 1 end 3 :1-328.N ###
For Eigenvector (1,2 and 3) vs Displacement for each N atom
crdaction crd1 projection modes evecs.dat out myproj.txt beg 1 end 3
:1-328.N #### For plot PC1vsPC2 or PC1vsPC3 etc.
2) Also how one can obtain two extreme configurations of system for whole
traj? Just by using lowest and highest rmsd with respect to average
structure or something one can do with PCA?
thanks
JIom
On Tue, May 6, 2014 at 6:24 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Mon, May 5, 2014 at 5:23 PM, newamber list <newamberlist.gmail.com>
> wrote:
> > 2) Also in many papers there are Principal component plots. If am not
> > wrong these are same obtained from 'projection modes' as shown below
> > (myproj.txt). Or its something else?
>
> The plots you refer to are actually histograms generated using the
> 'hist' command of the principal component projections obtained from
> the 'projection' command, see the bottom of the script in
>
> http://pubs.acs.org/doi/suppl/10.1021/ct400862k/suppl_file/ct400862k_si_001.pdf
> .
>
> > trajin 1trj.nc
> > trajin 2trj.nc
> > rms first :1-328.N
> > average Avg.rst7 ncrestart
> > createcrd crd1
> > run
> >
> > reference Avg.rst7.1 [avg]
> > crdaction crd1 rms ref [avg] :1-328.N
> > crdaction crd1 matrix covar :1-328.N name myCovar
> > runanalysis diagmatrix myCovar out evecs.dat vecs 15
> >
> > readdata evecs.dat
> > crdaction crd1 projection modes evecs.dat out myproj.txt beg 1 end 3
> :1-328.N
>
> The last 'projection' command will create 3 data sets (corresponding
> to projections for PCs 1, 2, and 3) which you can then histogram,
> either with cpptraj or your favorite program. It will be probably be
> easier to histogram within cpptraj if you name the 'projection' data
> sets, e.g.:
>
> crdaction crd1 projection P1 modes evecs.dat out myproj.txt beg 1 end 3
> :1-328.N
> runanalysis hist P1:1,*,*,*,100 out pca.hist.agr norm name P1-1
>
> etc. See the manual for more details on the 'hist' command (or
> alternatively the 'kde' command to use a kernel density estimator
> instead).
>
> Hope this helps,
>
> -Dan
>
> >
> > Thanks
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue May 06 2014 - 19:30:02 PDT
