#!/bin/csh -f
########################################################################
# Atomic positional fluctuations of atoms.
# Two-step procedure:
#   1. Calculate average coordinates for molecule of interest.
#      Coordinate sets are aligned on ALL atoms of the first set.
#   2. Calculate mean deviation from averaged structure (atomic positional 
#      fluctuations). Coordinate sets are aligned on ALL atoms of 
#      average coordinates.
#
#  Peter Slickers, IMB Jena, 14 May 1998
#
#  Comment by Bill Ross: 
#   Note that in this example Peter uses as input a trajectory with
#   waters and box stripped, so he provides NOBOX and ATOM information
#   to the STREAM definition so that he can use the prmtop that has
#   waters and box defined.
########################################################################
set TABLE                =  fluctuation.tab
set TOPO                 =  cplx.prm.top
set TRAJECTORY           =  extract.xyz
########################################################################
set ATOM_NUMBER = 820
########################################################################

###### Carnal run 1:
echo "Calculate Reference structure by averaging rms fit to 1st set:"
$AMBER/exe/carnal -O <<_ende_   || exit(1)

FILES_IN
  PARM     p1        ${TOPO};
  STREAM   str       NOBOX  ATOM  ${ATOM_NUMBER}  ${TRAJECTORY};

FILES_OUT
  COORD    average   temp.average.pdb PDB;

DECLARE
  GROUP    all       (ATOM 1-${ATOM_NUMBER});
  RMS      fit_all   FIT all  str;
  
OUTPUT
  COORD    average   fit_all   AVERAGE; 

END
_ende_
########################################################################

###### Carnal run 2:
echo "Fit coords to reference structure:"
$AMBER/exe/carnal -O <<_ende_   || exit(1)

FILES_IN
  PARM     p1          ${TOPO};

## STREAM:     First set of str is used as reference for rms fit.
  STREAM   str         NOBOX  ATOM  ${ATOM_NUMBER}  
                       temp.average.pdb
                       ${TRAJECTORY};

FILES_OUT
  TABLE    table  ${TABLE};


DECLARE
# RMS Alignment creating new stream:
  GROUP   all      (ATOM 1-${ATOM_NUMBER});
  RMS     fit_all  FIT all  str;
  
OUTPUT
  TABLE    table    fit_all%atoms; 


END
_ende_
########################################################################
/bin/rm -f  temp.average.xyz
exit(0)
########################################################################
# eof