Hi,
On Fri, Jul 26, 2013 at 8:53 AM, Hongyi WU <why0713.sjtu.edu.cn> wrote:
> But can I define different masks for different residues in this command?
You can't, it is by definition a symmetric matrix.
> I have already tried "crosscor", another command you mentioned to me, like
> this:
> Parm R.prmtop
> trajin R.mdcrd
> vector v1 center :1.N
> vector v2 center :2.CB
> crosscor v1 v2 out 1_2.crosscor
>
> But I get all zeros.
Unfortunately the 'crosscorr' command currently works with non-vector
data sets only. I think probably your best bet at this point is to use
'matrix correl' with a mask that encompasses all of the atoms you wish
to look at, e.g.:
matrix correl name correlation :1.N,:2.CB out correl.matrix
In this case the off-diagonal elements in 'correl.matrix' will contain
the information you want.
-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)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jul 27 2013 - 10:00:02 PDT
