In addition to 'diagmatrix', you may be interested in the 'modes'
analysis and/or 'projection' action for further analysis of your
resulting eigenvalues/eigenvectors. Also, remember to remove your
global translational/rotational motion if you don't want that included
in your results by performing e.g. an RMS fit to the averaged
structure prior to calculating your matrix.
Recent examples of performing PCA (among other types of analysis) with
CPPTRAJ can be found in the supporting information of these papers:
http://pubs.acs.org/doi/abs/10.1021/ct400862k
http://pubs.acs.org/doi/abs/10.1021/jp4125099
-Dan
On Tue, Apr 29, 2014 at 9:55 AM, Andre C. Stiel
<andre.stiel.tuebingen.mpg.de> wrote:
> I do something like the following in cpptraj:
>
> matrix covar name covar_mat byatom .CA # to get the covar matrix
> (in this case not mass weighted)
> go
> diagmatrix covar_mat out covar_ca.matrix.modes vecs 1023 # to get the
> diagonalization and by that the vectors
> go
>
> more details on that in the cpptraj description in the Ambertools manual
>
> cheers
>
>
> On 04/29/2014 05:40 PM, Ibrahim Said wrote:
>> Dear Amber user
>> Please, how can I get the eigenvectors and eigenvalues from mwcvmat.dat
>> file.
>> I calculated the mass-weighted matrix for CA atoms of my protein.
>>
>> Thank you in advance
>>
>> Ibrahim
>> _______________________________________________
>> 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
Received on Tue Apr 29 2014 - 09:30:02 PDT
