Example: amsprep: Replace atom with ligandΒΆ

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

# 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