lachele@rime:~/RESEARCH/DLIVE/scripts$ diff make_cpptraj_files.bash make_cpptraj_files_d4m.bash
10a11,18
> ## Fix the number of atoms in the prod.nc file
> 	echo "trajin ../${i}/prod.nc  [traj${i}] " > all_cpptraj_${i}p.in 
> 	echo "" >> all_cpptraj_${i}p.in 
> 	echo "strip :WAT " >> all_cpptraj_${i}p.in
> 	echo "trajout ../${i}/prods.nc netcdf " >> all_cpptraj_${i}p.in
> 	echo "go" >>all_cpptraj_${i}p.in
> 
> 
12c20
< 	echo "trajin ../${i}/prod.nc  [traj${i}] " > all_cpptraj_${i}.in 
---
> 	echo "trajin ../${i}/prods.nc  [traj${i}] " > all_cpptraj_${i}.in 
60a69
> 	${AMBERHOME}/bin/cpptraj -i all_cpptraj_${i}p.in -p ../input/plus8water.parm7