# Strip water (but leave ions) in full.prmtop and full.equil.crds
cpptraj -i cppt-strip.in
# Convert nowat prmtop/crds to .top/.gro
$AMBERHOME/miniconda/bin/python convert2gro.py
### Convert to .tpr
gmx_d grompp -f example.mdp -c nowat.gro -p nowat.top -o nowat.tpr > & log.grompp
### Make human readable
gmx_d dump -s nowat.tpr > nowat.tpr.txt

### grep angles, dihedrals, and LJ
grep =ANGLES, nowat.tpr.txt | sed 's/,//g' | awk '{printf "%s %9.4f %s %9.4f\n",$2,$3,$4,$5}' | sort -k2,2n -k4,4n > nowat.ANGLES.txt
grep =PDIHS, nowat.tpr.txt | sed 's/,//g' | awk '{printf "%s %8.3f %s %9.4f %s\n",$2,$3,$4,$5,$10}' | sort -k2,2n -k4,4n > nowat.PDIHS.txt
grep LJ_SR nowat.tpr.txt | sed 's/,//g' | awk '{printf "%s %12.5e %s %12.5e\n",$2,$3,$4,$5}' | sort -k2,2g -k4,4g > nowat.LJ_SR.txt

### Convert Elcock's .tpr to human readable and grep parameters
gmx_d dump -s rApA_plus_ions.tpr > rApA_plus_ions.tpr.txt
grep =ANGLES, rApA_plus_ions.tpr.txt | sed 's/,//g' | awk '{printf "%s %9.4f %s %9.4f\n",$2,$3,$4,$5}' | sort -k2,2n -k4,4n > rApA.ANGLES.txt
grep =PDIHS, rApA_plus_ions.tpr.txt | sed 's/,//g' | awk '{printf "%s %8.3f %s %9.4f %s\n",$2,$3,$4,$5,$10}' | sort -k2,2n -k4,4n > rApA.PDIHS.txt
grep LJ_SR rApA_plus_ions.tpr.txt | sed 's/,//g' | awk '{printf "%s %12.5e %s %12.5e\n",$2,$3,$4,$5}' | sort -k2,2g -k4,4g > rApA.LJ_SR.txt


### Now diff the files
diff -y -W 150 nowat.ANGLES.txt rApA.ANGLES.txt
diff -y -W 150 nowat.PDIHS.txt rApA.PDIHS.txt
diff -y -W 150 nowat.LJ_SR.txt rApA.LJ_SR.txt


