On Mon, Apr 21, 2014 at 2:19 AM, Setyanto Md <stwahyudi.md.gmail.com> wrote:
> Why you named the average structure with "avgStruct.rst7", the number "7"
> could be replaced or it is mandatory ?
It's mandatory if you want the format (in this case Amber restart) to
be auto-detected from the name; otherwise you need to add the
'restart' format key after the filename (see Amber14 manual table 28.3
for a list of keywords/extensions).
> can we named the average structure wit avgStruct.pdb ?
You can use any format cpptraj recognizes. I use the restart format
because the coordinates have a higher precision than what's possible
in PDB files (actually if you want even more precision NetCDF restart
is best), but it probably doesn't matter to the overall results in
this case; any differences will be round-off.
-Dan
>
> Thank you
> Setyano Tri Wahyudi
>
>
> On Mon, Apr 14, 2014 at 10:20 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> Hi,
>>
>> I assume what you want is to calculate histograms of the projection of
>> your coordinates along the first two PCs? If so, you just need to use
>> the 'projection' action followed by 'hist' analysis. This can be done
>> with the following commands:
>>
>> rms first :1-18.CA
>> projection modes evecs-ca_10.dat start 1 stop 2 .CA myproj
>> hist myproj:1 bins 200 out PC.hist.agr
>> hist myproj:2 bins 200 out PC.hist.agr
>>
>> Modify the histogram commands as needed (e.g. put both data sets in
>> the same command for a 2D histogram etc). Note that the coordinates
>> (and mask you use) for the 'projection' command should be the same as
>> when you generated the original covariance matrix, but the
>> 'center'/'image' commands are not needed since the 'rms' command
>> changes the coordinates of interest anyway.
>>
>> This entire procedure can actually be done in a single cpptraj run by
>> saving the coordinates as a COORDS data set and making a few passes
>> over it with 'crdaction' like so:
>>
>> rms first :1-18.CA
>> average avgStruct.rst7
>> createcrd crd1 # Creates COORDS data set crd1
>> run
>> reference avgStruct.rst7.1
>> crdaction crd1 rms reference :1-18.CA
>> crdaction crd1 matrix out matrix.dat name mymatrix covar .CA
>> runanalysis diagmatrix mymatrix out evecs.dat vecs 10 name mymodes
>> crdaction crd1 projection modes evecs.dat start 1 stop 2 .CA myproj
>> hist myproj:1 bins 200 out PC.hist.agr
>> hist myproj:2 bins 200 out PC.hist.agr
>>
>> Note that here I am RMS-fitting to an averaged structure, which should
>> do a better job of eliminating global rotations (I assume you have a
>> reason for making the fitting mask and matrix masks separate so I kept
>> that in my example). Note that in the upcoming release of cpptraj you
>> will actually be able to use the 'modes' data set generated by the
>> 'diagmatrix' command directly with the 'projection' action rather than
>> having to read it back in.
>>
>> Hope this helps,
>>
>> -Dan
>>
>> On Mon, Apr 14, 2014 at 5:45 AM, Neha Gandhi <n.gandhiau.gmail.com> wrote:
>> > Hi List,
>> >
>> > I have calculated PCA using following to output file containing 10
>> models.
>> > center origin :1-18
>> > # now image the whole system about the centered origin
>> > image origin center
>> > rms first :1-18.CA
>> > matrix covar name covmat out covmat-ca_10.dat .CA
>> > analyze matrix covmat out evecs-ca_10.dat vecs 10
>> >
>> > This seem like a trivial question. How do I read these models (PCA 1 to
>> 2)
>> > to define datasets in the hist (histogram) command in cpptraj?
>> >
>> > Many thanks,
>> > Neha
>> > _______________________________________________
>> > 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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> 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 Mon Apr 21 2014 - 08:00:02 PDT
