JoaoRodrigues

#!/bin/bash

for folder in `ls $1`; do

  echo "Peeking into ${folder}"

  if [ ! -e ${1}/${folder}/md.log ]; then
    echo "!! No md.log in here"
    continue
  fi

  if [ -e ${1}/last_frames/${folder}.pdb ]; then
    echo "Already dumped and saved!"
    continue
  fi

  # Extract relevant index ( 0 for system )

  # toto.txt is just a txt file with keep 0\nq

  make_ndx -o ${1}/${folder}/traj.ndx -f ${1}/${folder}/conf.gro < toto.txt &> /dev/null

  # Extract last step (This works for l-BFGS integrators! The grep will fail otherwise)
  fstep=`grep "Low-Memory BFGS Minimizer converged" ${1}/${folder}/md.log | awk '{ print $(NF-1) }'`

  # Dump PDB & Copy to special directory
  trjconv -f ${1}/${folder}/traj.trr -s ${1}/${folder}/topol.tpr -n ${1}/${folder}/traj.ndx -o ${1}/${folder}/${folder}.pdb -dump $fstep &> ${1}/${folder}/d$

  cp ${1}/${folder}/${folder}.pdb ${1}/last_frames/${folder}.pdb

  echo "PDB File dumped and saved"
done
exit