Hi,
On Fri, Apr 12, 2013 at 5:25 AM, anu chandra <anu80125.gmail.com> wrote:
> To capture the correlation between such side-chain conformations, is it
> possible to do a correlation of side-chain dihedral angles ( for e.g.
> dynamic correlation of chi1 angle ) using PTRAJ?. If so, how can I proceed
> further for make a PTRAJ script for the same?
Unfortunately it's not currently possible to calculate dihedral
correlations with ptraj.
> Is it possible to have a similar approach in case of bond vectors ( for
> e.g, dynamic correlation of CA-CB vector )
You can calculate auto and cross time correlation functions for
vectors in ptraj/cpptraj with the 'vector' and 'analyze timecorr'
commands. See the manual for further details.
-Dan
--
-------------------------
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 Mon Apr 15 2013 - 07:30:04 PDT
