AMBER

Setup with tleap
Check bonds

Use the "desc" command (syntax: See above)x=loadpdb pdb.in3

desc x.692.FE

desc x.694.F

General syntax: pdbnme.resnumber.atomname

Add bonds

Use the "bond" command (syntax: See above)

x=loadpdb pdb.in3

bond x.156.SG x.206.SG