( ( After ( ( the ( connectivity table ) ) ( is created ) ) ) ( , ( ( atom ( ( types and ) charges ) ) ( ( set ( for ( ( nonbonding ( interactions ( and ( bonding ( energy ( terms lists ) ) ) ) ) ) ( can ( be created ) ) ) ) ) . ) ) ) )
(ROOT (S (SBAR (IN After) (S (NP (DT the) (JJ connectivity) (NN table)) (VP (VBZ is) (VP (VBN created))))) (, ,) (NP (NN atom) (NNS types) (CC and) (NNS charges)) (VP (VBD set) (SBAR (IN for) (S (NP (JJ nonbonding) (NNS interactions) (CC and) (NN bonding) (NN energy) (NNS terms) (NNS lists)) (VP (MD can) (VP (VB be) (VP (VBN created))))))) (. .)))
After the connectivity table is created, atom types and charges set for nonbonding interactions and bonding energy terms lists can be created.
(ROOT (S (NP (NN Bond) (NN energy)) (VP (VBZ holds) (NP (NNS atoms)) (ADVP (RB together))) (. .)))
Bond energy holds atoms together.