Example: amsprep: Replace atom with ligand
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"Download LoopAtomsLigands.run"

   #! /bin/sh

   # generate a run file for methane, with 1 H replaced by some ligand (run amsprep
   # -liststructures to get full list of available structures) note the -a flag
   # makes amsprep produce an .ams file as well, which can be opened by AMSinput to
   # check your system

   for ligand in CN CO CO3 NC NH2 NH2CH3 NH3 OC OCH3 OH PH3 Pyridine; do
       "$AMSBIN/amsprep" -t GO -m "$AMSHOME/examples/adf/LoopAtomsLigands/methane.xyz" -structure "2 Ligands/$ligand.ams" -a methane.$ligand.ams
   done

   # similar, replace the C atom by other atoms

   for atom in C Si Ge Sn Pb; do
       "$AMSBIN/amsprep" -t GO -m "$AMSHOME/examples/adf/LoopAtomsLigands/methane.xyz" -atomtype "1 $atom" -a methane.$atom.ams
   done
