#!/bin/sh
#
# create the appropriate AMBER input *RST file from .7clm file and
# DG input. 

if [ "$#" -ne 1 ]
then
   prgName=`basename $0`
   echo "Usage: $prgName [7col.comb.one file]"
   exit 1
fi

if [ ! -r $1 ]
then
   echo "Cannot read $1"
   exit 1
fi

if [ -d mdprep ]
then
   if [ -d mdprep.old ]
   then
      rm -rf ./mdprep.old
   fi
   mv ./mdprep ./mdprep.old
fi
mkdir mdprep

/bin/cp $1 mdprep/7col.comb.intra
cat mdprep/7col.comb.intra > mdprep/f36g.tropp
noeconv -noe mdprep/f36g.tropp \
        -pdb sample.f36g.pdb \
        -map /home/mnelson/bin/md/map.DIANA-AMBER \
        -rst mdprep/f36g.noe.RST \
        -prm mdprep/f36g.PARMIN \
        -rm6 mdprep/f36g.RM6NOE

#/bin/cp f36g.hbond.8 mdprep/f36g.hbond
#cat mdprep/f36g.hbond \
#      | awk '{print $1, $2, $3, $4, $5, $6, $8}' \
#      > mdprep/f36g.hbond.7
#noeconv -noe mdprep/f36g.hbond.7 \
#        -pdb /home/mnelson/bin/md/sample.f36g.pdb \
#        -map /home/mnelson/bin/md/map.DIANA-AMBER \
#        -rst mdprep/f36g.hbond1.RST \
#        -prm mdprep/f36g.hbond.PARMIN \
#        -rm6 mdprep/f36g.hbond.RM6NOE
#/bin/rm mdprep/f36g.hbond.7
#fixhbondbounds -h mdprep/f36g.hbond -r mdprep/f36g.hbond1.RST \
#      > mdprep/f36g.hbond.fix
#/bin/mv mdprep/f36g.hbond.fix mdprep/f36g.hbond.RST

# phi file should not containt the flat ring constraints...
/bin/cp f36g.aco mdprep/f36g.aco
diana2habas mdprep/f36g.aco > mdprep/f36g.phi.aco
habmdconv sample.f36g.pdb \
      mdprep/f36g.phi.aco > mdprep/f36g.dihed.RST
checkconst mdprep/f36g.phi.aco

mk_chir_cons sample.f36g.pdb mdprep/f36g.chirality.RST

# Merge the restraints
echo "# f36g.noe.RST" > mdprep/f36g.RST
cat mdprep/f36g.noe.RST >> mdprep/f36g.RST
#echo "# f36g.hbond.RST" >> mdprep/f36g.RST
#cat mdprep/f36g.hbond.RST >> mdprep/f36g.RST
echo "# f36g.dihed.RST" >> mdprep/f36g.RST
cat mdprep/f36g.dihed.RST >> mdprep/f36g.RST
echo "# f36g.chirality.RST" >> mdprep/f36g.RST
cat mdprep/f36g.chirality.RST >> mdprep/f36g.RST

RM6noecount mdprep/f36g.noe.RST
constcount mdprep/f36g.phi.aco