#!/bin/bash

# Check the existence of a test version of the mdgx program
MDGX="${AMBERHOME}/bin/mdgx"
if [ -n "${TESTmdgx}" ] ; then
  MDGX=${TESTmdgx}
  echo "MDGX set to ${MDGX}"
fi

# Write a charge fitting input file
cat > fit.in << EOF
&files
  -p     vALADi.top
  -o     fit.out
&end

&fit
  phi1  ala1.cube   -p1 vALADi.top
  phi2  ala2.cube   -p2 vALADi.top
  phi3  glu1.cube   -p3 vGLUDi.top
  phi4  glu2.cube   -p4 vGLUDi.top
  phi5  thr1.cube   -p5 vTHRDi.top
  phi6  thr2.cube   -p6 vTHRDi.top
  pnrg          0.0
  flim          0.39
  nfpt          100
  equalq1       '(!:ACE,NME) & @O'
  equalq2       '(!:ACE,NME) & @N'
  equalq3       '(!:ACE,NME) & @C'
  equalq4       '(!:ACE,NME) & @H'
  equalq5       ':ACE & @HH31,HH32,HH33'
  equalq6       ':ACE & @CH3'
  equalq7       ':ACE & @C'
  equalq8       ':ACE & @O'
  equalq9       ':NME & @HH31,HH32,HH33'
  equalq10      ':NME & @CH3'
  equalq11      ':NME & @N'
  equalq12      ':NME & @H'
  equalq13      ':ALA & @HB1,HB2,HB3'
  equalq14      ':GLU & @HB2,HB3'
  equalq15      ':GLU & @HG2,HG3'
  equalq16      ':GLU & @OE1,OE2'
  equalq17      ':THR & @HG11,HG12,HG13'
  minq1         ':NME & @CH3'
  minq2         ':ACE & @CH3'
  minq3         '@CB'
  minqwt        1.0e-2
  sumq1         ':NME'
  sumq2         ':ACE'
  groupqtot1    0.0
  groupqtot2    0.0
  CFExtension   pdb
  hist          fqpt.dat
  Verbose       0
&end
EOF

# Run the mdgx program
${MDGX} -O -i fit.in

# Analyze the relevant output
grep "^ HH31" fit.out > hydrogenQ.dat

${AMBERHOME}/AmberTools/test/dacdif hydrogenQ.dat.save hydrogenQ.dat
${AMBERHOME}/AmberTools/test/dacdif fqpt.dat.save fqpt.dat
/bin/rm -f fit.in fit.out *.pdb hist.dat