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
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
|