#!/bin/bash
# extract confs generated in step 3 for the PF-3CLpro complex

module load profile/lifesc autoload gromacs/2019.6

mkdir conf

# loop on batteries dirs

for i in {0..5}; do
          echo "0" | gmx trjconv -f /BATTERY$i/scaled0/traj_comp.xtc -s /BATTERY$i/scaled0/HREM.tpr -pbc mol -ur  compact -b 2000 -skip 8 -sep -o conf/conf"$i"_.pdb 
done