( ( The ( atom type ) ) ( ( determines ( ( the ( energy parameters ) ) ( used ( in ( calculating ( ( ( the ( non-bond ( contact energy ) ) ) ( -LRB- ( ( in ( the ( PEGASUS program ) ) ) -RRB- ) ) ) ( for ( interactions ( involving ( that ( particular atom ) ) ) ) ) ) ) ) ) ) ) . ) )
(ROOT (S (NP (DT The) (NN atom) (NN type)) (VP (VBZ determines) (NP (NP (DT the) (NN energy) (NNS parameters)) (VP (VBN used) (PP (IN in) (S (VP (VBG calculating) (NP (NP (DT the) (JJ non-bond) (NN contact) (NN energy)) (PRN (-LRB- -LRB-) (PP (IN in) (NP (DT the) (NNP PEGASUS) (NN program))) (-RRB- -RRB-)) (PP (IN for) (NP (NP (NNS interactions)) (VP (VBG involving) (NP (DT that) (JJ particular) (NN atom)))))))))))) (. .)))
The atom type determines the energy parameters used in calculating the non-bond contact energy (in the PEGASUS program) for interactions involving that particular atom.
(ROOT (S (NP (NN Bond) (NN energy)) (VP (VBZ holds) (NP (NNS atoms)) (ADVP (RB together))) (. .)))
Bond energy holds atoms together.