>> It's not clear what you mean here - which file had 11 columns? Can you
post the exact input you are using, and point out the file that you
unsure about that has 11 columns?
This is the command line I have used
diagmatrix systemcovar out evectors.dat vecs 20 nmwiz nmwizvecs 5
nmwizfile system.nmd nmwizmask :1-831.CA
>>>Yes. You are projecting the coordinates of CA atoms of residues 1-831
on the eigenvectors read in from evectors.dat (presumably generated
from the same coordinate selection), only for eigenvectors (modes) 1
and 2
So In that case, in my PC1 vs PC2, each point represents one frame?
On Tue, 20 Jul 2021 at 23:41, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Fri, Jul 16, 2021 at 3:43 PM Jenny 148 <jenny.rs140.gmail.com> wrote:
> > I am working with a protein system. I have constructed the
> > diagonalized coordinate covariance matrix for eigenmodes in a file
> > evectors.dat with the command line being beg 1 end 20 (though I had only
> 11
> > columns, the reason of which I am not sure. After that using the
> following
>
> It's not clear what you mean here - which file had 11 columns? Can you
> post the exact input you are using, and point out the file that you
> unsure about that has 11 columns?
>
> > readdata evectors.dat name Modes
> > # Now create separate PC projections for each trajectory
> > projection A1 modes Modes out pca12-ca beg 1 end 2 :1-831.CA
> >
> > After which I get a file pca12-ca, which looked somewhat like this:
> > #Frame Mode1 Mode2
> > 1 36.824 5.205
> > 2 35.917 5.359
> > 3 34.797 6.404
> > 4 34.637 8.611
> > 5 35.224 9.040
> > ...........(Blanking out the rest)
> >
> > My query is whether the pca12-ca file which I got, the actual PC1 vs PC2
> > file? I mean, would plotting the 2nd and 3rd column in the above file
> as X
> > and Y axis, allow me to get a scatter plot between the First and second
>
> Yes. You are projecting the coordinates of CA atoms of residues 1-831
> on the eigenvectors read in from evectors.dat (presumably generated
> from the same coordinate selection), only for eigenvectors (modes) 1
> and 2.
>
> Hope this helps,
>
> -Dan
>
> > principal component of my trajectory?
> >
> > --
> > Jenny R.S
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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>
--
Jenny R.S
Sir Syed College,
Taliparamba,
Kannur,
Kerala
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Received on Wed Jul 21 2021 - 01:00:02 PDT
