On Tue, May 6, 2014 at 10:21 PM, newamber list <newamberlist.gmail.com> wrote:
> 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
If you are referring to figures 3/4 in the above reference, then what
you want to calculate is the projection of your coordinates along
certain eigenvectors - see the 'projection' command in CPPTRAJ. The
'modes displ' just calculates total XYZ displacement for all
eigenvectors.
-Dan
> )
>
> 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)
>> >>
>> >> _______________________________________________
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>> >>
>> > _______________________________________________
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>>
>>
>>
>> --
>> -------------------------
>> 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
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
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> 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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Received on Wed May 07 2014 - 08:00:09 PDT
