AMBER Archive (2005)

Subject: Re: AMBER: carnal problem

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Fri Apr 15 2005 - 13:42:16 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

It seems that ALL should have picked up the PLANE, tho MEAS
would not ("MEAS ... prints all scalar measurements"). Which
version of amber are you using?

I would try:

 OUTPUT
  TABLE tab1 pla1;

Bill
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