Hi,
I think what you want is the correlation matrix calculation or 'matrix
correl'. This calculates matrix entries as:
Mij = (<ri * rj> - <ri><rj>) / sqrt( (<ri^2> - <ri>^2) * (<rj^2> - <rj>^2) )
which I believe is the definition commonly defined as a dynamic
cross-correlation map (DCCM). In order to get meaningful results you
should probably RMS-fit your structures to an average structure first
(otherwise translational and rotational motions will dominate). So a
typical procedure might go (assuming you have a previously calculated
average reference structure or something similar):
reference average.rst7
trajin traj.nc
rms reference .CA
matrix correl .CA out matrix_correl_CA.dat
If you would like the output by residue specify the 'byres' keyword in
the 'matrix' command. Hope this helps,
-Dan
On Wed, Jun 12, 2013 at 7:22 PM, #YIP YEW MUN# <YIPY0005.e.ntu.edu.sg> wrote:
> Hi,
>
> I wish to ask the steps to using ptraj in generating DCCM for alpha-C in
> proteins. I tried searching the net for a tutorial or some sort but to no
> avail. I would appreciate if there is someone to list out the step-by-step
> way to generating DCCM.
>
> Many thanks.
>
> --
> Regards
> Yip Yew Mun
> Chemistry and Biological Chemistry
> School of Physical and Mathematical Sciences
> Nanyang Technological University
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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) 585-9119 (Fax)
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Received on Thu Jun 13 2013 - 08:30:02 PDT
