Hi Dan,
It works, thanks.! It took me quite a while to search for the way to do correlation matrix calculation. =)
Regards
Yip Yew Mun
Chemistry and Biological Chemistry
School of Physical and Mathematical Sciences
Nanyang Technological University
On 13-Jun-2013, at 11:17 PM, Daniel Roe wrote:
> 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
>> _______________________________________________
>> 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) 585-9119 (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
Received on Sat Jun 15 2013 - 06:30:04 PDT
