Examples

A simple FLIP command file

INFILE
OUTFILE
COMM This file will flip atom number 1, keeping 2 and 3
COMM unchanged and swapping 4 and 5.
FLIP 1 2 3 4 5

A simple CHNG command file

INFILE
OUTFILE
COMM This file will change atom number 1 into a phenyl group
CHNG 2 1 4 0 0

A more complicated change

INFILE
OUTFILE
COMM This file will change a methyl group into a benzyl
COMM group, and explore the conformations of the benzyl
COMM group by rotating around the O-CH2 bond. The structure
COMM is: O(1)-C(2)H(3)H(4)H(5)
CHNG 2 3 4 0 0
WRIT
ROTA 1 2 120.0
WRIT
ROTA 1 2 120.0