# solve protein structure using NMR distance constraints #compare results to 1UAO.short.pdb . protein A 1 GYDPETGTWG firstStage 1 lastStage 1 # turn on MD force field terms: globalAmberImproperTorsionScaleFactor 1 globalBondBendScaleFactor 1 globalBondStretchScaleFactor 1 globalBondTorsionScaleFactor 1 globalCoulombScaleFactor 1 globalVdwScaleFactor 1 temperature 100 # These distance constraints came from 1UAO-disre-simple.txt: atomTether A 7 N A 3 O .3500 300.00 atomTether A 7 H A 3 O .2500 300.00 atomTether A 1 2HA A 2 H .3500 300.00 atomTether A 1 2HA A 9 HE3 .4500 300.00 atomTether A 1 2HA A 9 HZ3 .4500 300.00 atomTether A 2 HA A 2 2HB .3500 300.00 atomTether A 2 HA A 2 HD1 .3500 300.00 atomTether A 2 HA A 2 HD2 .3500 300.00 atomTether A 2 HA A 2 HE1 .6000 300.00 atomTether A 2 HA A 2 HE2 .6000 300.00 atomTether A 2 HA A 2 H .4500 300.00 atomTether A 2 2HB A 2 HD1 .3500 300.00 atomTether A 2 2HB A 2 HD2 .3500 300.00 atomTether A 2 2HB A 2 H .3500 300.00 atomTether A 2 HD1 A 2 H .4500 300.00 atomTether A 2 HD2 A 2 H .4500 300.00 atomTether A 2 HA A 3 H .2800 300.00 atomTether A 2 2HB A 3 H .6000 300.00 atomTether A 2 HD1 A 3 H .4500 300.00 atomTether A 2 HD2 A 3 H .4500 300.00 atomTether A 2 HE1 A 3 HA .6000 300.00 atomTether A 2 HE2 A 3 HA .6000 300.00 atomTether A 2 HE1 A 3 H .6000 300.00 atomTether A 2 HE2 A 3 H .6000 300.00 atomTether A 2 H A 3 H .6000 300.00 atomTether A 2 2HB A 4 2HD .4500 300.00 atomTether A 2 HD1 A 4 HA .4500 300.00 atomTether A 2 HD2 A 4 HA .4500 300.00 atomTether A 2 HD1 A 4 2HB .6000 300.00 atomTether A 2 HD2 A 4 2HB .6000 300.00 atomTether A 2 HD1 A 4 2HD .4500 300.00 atomTether A 2 HD2 A 4 2HD .4500 300.00 atomTether A 2 HD1 A 4 2HG .4500 300.00 atomTether A 2 HD2 A 4 2HG .4500 300.00 atomTether A 2 HE1 A 4 HA .3500 300.00 atomTether A 2 HE2 A 4 HA .3500 300.00 atomTether A 2 HE1 A 4 2HB .4500 300.00 atomTether A 2 HE2 A 4 2HB .4500 300.00 atomTether A 2 HD1 A 7 H .6000 300.00 atomTether A 2 HD2 A 7 H .6000 300.00 atomTether A 2 HE1 A 7 2HA .4500 300.00 atomTether A 2 HE2 A 7 2HA .4500 300.00 atomTether A 2 HE1 A 7 H .6000 300.00 atomTether A 2 HE2 A 7 H .6000 300.00 atomTether A 2 HD1 A 8 HA .6000 300.00 atomTether A 2 HD2 A 8 HA .6000 300.00 atomTether A 2 HE1 A 8 HA .4500 300.00 atomTether A 2 HE2 A 8 HA .4500 300.00 atomTether A 2 HE1 A 8 H .6000 300.00 atomTether A 2 HE2 A 8 H .6000 300.00 atomTether A 2 HA A 9 HA .4500 300.00 atomTether A 2 HA A 9 HE3 .4500 300.00 atomTether A 2 2HB A 9 HZ3 .6000 300.00 atomTether A 2 HD1 A 9 HA .4500 300.00 atomTether A 2 HD2 A 9 HA .4500 300.00 atomTether A 2 HD1 A 9 2HB .6000 300.00 atomTether A 2 HD2 A 9 2HB .6000 300.00 atomTether A 2 HD1 A 9 HD1 .4500 300.00 atomTether A 2 HD2 A 9 HD1 .4500 300.00 atomTether A 2 HD1 A 9 HE1 .4500 300.00 atomTether A 2 HD2 A 9 HE1 .4500 300.00 atomTether A 2 HD1 A 9 HE3 .6000 300.00 atomTether A 2 HD2 A 9 HE3 .6000 300.00 atomTether A 2 HD1 A 9 HH2 .6000 300.00 atomTether A 2 HD2 A 9 HH2 .6000 300.00 atomTether A 2 HD1 A 9 H .6000 300.00 atomTether A 2 HD2 A 9 H .6000 300.00 atomTether A 2 HD1 A 9 HZ2 .6000 300.00 atomTether A 2 HD2 A 9 HZ2 .6000 300.00 atomTether A 2 HD1 A 9 HZ3 .6000 300.00 atomTether A 2 HD2 A 9 HZ3 .6000 300.00 atomTether A 2 HE1 A 9 HD1 .6000 300.00 atomTether A 2 HE2 A 9 HD1 .6000 300.00 atomTether A 2 HE1 A 9 HE1 .6000 300.00 atomTether A 2 HE2 A 9 HE1 .6000 300.00 atomTether A 2 HE1 A 9 H .6000 300.00 atomTether A 2 HE2 A 9 H .6000 300.00 atomTether A 2 H A 9 HE3 .6000 300.00 atomTether A 2 H A 9 HZ3 .6000 300.00 atomTether A 3 HA A 3 2HB .4500 300.00 atomTether A 3 HA A 3 H .4500 300.00 atomTether A 3 2HB A 3 H .3500 300.00 atomTether A 3 HA A 4 2HD .4500 300.00 atomTether A 3 H A 4 2HD .6000 300.00 atomTether A 3 HA A 5 H .4500 300.00 atomTether A 3 2HB A 5 H .6000 300.00 atomTether A 3 2HB A 6 1HG2 .4500 300.00 atomTether A 3 2HB A 6 2HG2 .4500 300.00 atomTether A 3 2HB A 6 3HG2 .4500 300.00 atomTether A 3 2HB A 6 H .4500 300.00 atomTether A 3 H A 6 1HG2 .6000 300.00 atomTether A 3 H A 6 2HG2 .6000 300.00 atomTether A 3 H A 6 3HG2 .6000 300.00 atomTether A 3 2HB A 7 H .4500 300.00 atomTether A 3 2HB A 8 HB .6000 300.00 atomTether A 3 2HB A 8 H .4500 300.00 atomTether A 3 H A 8 H .4500 300.00 atomTether A 4 HA A 4 2HB .3500 300.00 atomTether A 4 2HB A 4 2HD .4500 300.00 atomTether A 4 2HB A 4 2HG .2800 300.00 atomTether A 4 2HD A 4 2HG .3500 300.00 atomTether A 4 HA A 5 H .4500 300.00 atomTether A 4 2HB A 5 H .6000 300.00 atomTether A 4 2HD A 5 H .6000 300.00 atomTether A 4 2HG A 5 HA .6000 300.00 atomTether A 4 2HG A 5 H .4500 300.00 atomTether A 4 HA A 6 H .6000 300.00 atomTether A 4 HA A 7 H .4500 300.00 atomTether A 5 HA A 5 2HB .3500 300.00 atomTether A 5 HA A 5 2HG .4500 300.00 atomTether A 5 HA A 5 H .3500 300.00 atomTether A 5 2HB A 5 2HG .2800 300.00 atomTether A 5 2HB A 5 H .3500 300.00 atomTether A 5 2HG A 5 H .4500 300.00 atomTether A 5 HA A 6 H .4500 300.00 atomTether A 5 2HB A 6 1HG2 .6000 300.00 atomTether A 5 2HB A 6 2HG2 .6000 300.00 atomTether A 5 2HB A 6 3HG2 .6000 300.00 atomTether A 5 2HB A 6 H .3500 300.00 atomTether A 5 2HG A 6 H .6000 300.00 atomTether A 5 H A 6 1HG2 .6000 300.00 atomTether A 5 H A 6 2HG2 .6000 300.00 atomTether A 5 H A 6 3HG2 .6000 300.00 atomTether A 5 H A 6 H .3500 300.00 atomTether A 5 HA A 7 H .6000 300.00 atomTether A 5 2HB A 7 H .6000 300.00 atomTether A 6 HA A 6 1HG2 .3500 300.00 atomTether A 6 HA A 6 2HG2 .3500 300.00 atomTether A 6 HA A 6 3HG2 .3500 300.00 atomTether A 6 HA A 6 H .4500 300.00 atomTether A 6 HB A 6 1HG2 .3500 300.00 atomTether A 6 HB A 6 2HG2 .3500 300.00 atomTether A 6 HB A 6 3HG2 .3500 300.00 atomTether A 6 HB A 6 H .4500 300.00 atomTether A 6 1HG2 A 6 H .4500 300.00 atomTether A 6 2HG2 A 6 H .4500 300.00 atomTether A 6 3HG2 A 6 H .4500 300.00 atomTether A 6 HA A 7 H .4500 300.00 atomTether A 6 HB A 7 H .4500 300.00 atomTether A 6 1HG2 A 7 2HA .6000 300.00 atomTether A 6 2HG2 A 7 2HA .6000 300.00 atomTether A 6 3HG2 A 7 2HA .6000 300.00 atomTether A 6 1HG2 A 7 H .6000 300.00 atomTether A 6 2HG2 A 7 H .6000 300.00 atomTether A 6 3HG2 A 7 H .6000 300.00 atomTether A 6 H A 7 H .3500 300.00 atomTether A 6 HB A 8 H .6000 300.00 atomTether A 7 2HA A 7 H .3500 300.00 atomTether A 7 2HA A 8 H .4500 300.00 atomTether A 7 H A 8 H .3500 300.00 atomTether A 8 HA A 8 HB .4500 300.00 atomTether A 8 HA A 8 1HG2 .4500 300.00 atomTether A 8 HA A 8 2HG2 .4500 300.00 atomTether A 8 HA A 8 3HG2 .4500 300.00 atomTether A 8 HA A 8 H .3500 300.00 atomTether A 8 HB A 8 1HG2 .3500 300.00 atomTether A 8 HB A 8 2HG2 .3500 300.00 atomTether A 8 HB A 8 3HG2 .3500 300.00 atomTether A 8 HB A 8 H .4500 300.00 atomTether A 8 1HG2 A 8 H .4500 300.00 atomTether A 8 2HG2 A 8 H .4500 300.00 atomTether A 8 3HG2 A 8 H .4500 300.00 atomTether A 8 HA A 9 HD1 .6000 300.00 atomTether A 8 HA A 9 HE3 .6000 300.00 atomTether A 8 HA A 9 H .3500 300.00 atomTether A 8 HB A 9 H .3500 300.00 atomTether A 8 1HG2 A 9 HD1 .6000 300.00 atomTether A 8 2HG2 A 9 HD1 .6000 300.00 atomTether A 8 3HG2 A 9 HD1 .6000 300.00 atomTether A 8 1HG2 A 9 H .4500 300.00 atomTether A 8 2HG2 A 9 H .4500 300.00 atomTether A 8 3HG2 A 9 H .4500 300.00 atomTether A 8 H A 9 H .4500 300.00 atomTether A 8 HB A 10 H .6000 300.00 atomTether A 9 HA A 9 2HB .4500 300.00 atomTether A 9 HA A 9 HD1 .6000 300.00 atomTether A 9 HA A 9 HE3 .4500 300.00 atomTether A 9 HA A 9 H .4500 300.00 atomTether A 9 2HB A 9 HD1 .4500 300.00 atomTether A 9 2HB A 9 HE3 .3500 300.00 atomTether A 9 2HB A 9 H .4500 300.00 atomTether A 9 2HB A 9 HZ3 .6000 300.00 atomTether A 9 HD1 A 9 H .4500 300.00 atomTether A 9 HE3 A 9 H .4500 300.00 atomTether A 9 HA A 10 H .3500 300.00 atomTether A 9 2HB A 10 H .4500 300.00 atomTether A 9 HE3 A 10 H .6000 300.00 atomTether A 9 H A 10 H .4500 300.00 atomTether A 10 2HA A 10 H .3500 300.00