AMBER Archive (2005)

Subject: Re: AMBER: carnal problem

From: Ed Pate (pate_at_math.wsu.edu)
Date: Fri Apr 15 2005 - 13:10:37 CDT

> > I have done a MD simulation and would like to examine the normal vector as
> > a function of time for three different atoms in the same residue. I
> > am trying to do this using CARNAL. From the manual, and my own attempts,
> > I gather that the vector formed by the PLANE command is not a MEAS that
> > can be output.
>
> It would be interesting to see what you tried. I think that if you
> list the plane in an OUTPUT TABLE statement the vector should appear
> in the table.
>
The script I used follows. What am I doing wrong? Thanks for the help.

# coordinates of spin ring to determine vector
FILES_IN
 PARM p1 xxx.top;
 STREAM s1 xxx_100ps.crd;
FILES_OUT
 TABLE tab1 vec100.tab;
DECLARE
 PLANE pla1 CC 745 ND 745 CE 745;
OUTPUT
 TABLE tab1 ALL;
END

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