Hi Daniel
Thanks
1)
>> Try using 'modes name evecs.dat ...'.
Its working now but I am not sure if this is how people calculate/present
their results. Usually in papers they show displacements along one
eigenvector (e.g.
http://pubs.rsc.org/en/Content/ArticleLanding/2014/MB/c4mb00177j#!divAbstract
)
I get displX, Y and Z but I was expecting some net displacement which
simply I think should be sqrt(x^2+y^+z^2) and also for each individual
eigenvector I should do something like this:
modes name evecs.dat displ out dis1.dat beg 1 end 1
modes name evecs.dat displ out dis2.dat beg 2 end 2
2)
>> If the only goal is to get two structures that look the least like each
other, one way is to calculate the 2D RMSD
This is nice suggestion indeed. I was following some previous amber archive
mails to generate procupine plots which needs two extreme pdbs in
discussion it was not mentioned how one can get two extremes.
best regards
On Wed, May 7, 2014 at 4:27 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> On Tue, May 6, 2014 at 8:13 PM, newamber list <newamberlist.gmail.com>
> wrote:
> > 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
> ###
>
> The problem here is that you are trying to use 'myCovar' (which is a
> matrix) as your modes data set, which by default will be called
> 'evecs.dat' since you did not supply a name. Try using 'modes name
> evecs.dat ...'.
>
> > 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?
>
> If the only goal is to get two structures that look the least like
> each other, one way is to calculate the 2D RMSD and find the pair of
> frames with the largest RMSD. You will probably want to use the
> 'nosquare2d' option with standard data output to make searching
> easier, e.g.
>
> 2drms .CA out rms2d.dat
> datafile rms2d.dat nosquare2d
>
> Hope this helps,
>
> -Dan
>
> >
> > 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)
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > 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)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue May 06 2014 - 21:30:02 PDT
