#!/bin/bash

mkdir scan

for dihedral in {0..39} ;do
  
  #specify the .mol file here and the atoms between which the dihedral angle is defined
  #I use a step size of 9 degrees per scan

 "$AMSBIN/amsprep" -t GO -m PyrDMA.mol -dihed "8 16 17 20 $((9*dihedral))"> "PyrDMA.txt"
  
  mkdir scan/angle"("$dihedral")"
  mv PyrDMA.txt scan/angle"("$dihedral")"/coord.txt

done


