remark topologyIOTEST.INP remark test the TOPOLOGY I/O remark by Axel Brunger, 16-AUG-84 topology MASS H 1.00800! hydrogen which can h-bond to neutral atom MASS HC 1.00800! ="= ="= ="= to charged atom MASS HT 1.00800! TIPS3P water hydrogen MASS C 12.01100! carbonyl carbon MASS CH1E 13.01900! extended atom carbon with one hydrogen MASS CH2E 14.02700! ="= ="= ="= two hydrogens MASS CH3E 15.03500! ="= ="= ="= three hydrogens MASS CR1E 13.01900! ="= ="= in an aromatic ring with one H MASS N 14.00670! peptide nitrogen with no hydrogens attached MASS NR 14.00670! nitrogen in an aromatic ring with no hydrogens MASS NP 14.00670! pyrole nitrogen MASS NH1 14.00670! peptide nitrogen bound to one hydrogen MASS NH2 14.00670! ="= ="= ="= two hydrogens MASS NH3 14.00670! nitrogen bound to three hydrogens MASS NC2 14.00670! charged guandinium nitrogen bound to two hydrogens MASS O 15.99940! carbonyl oxygen MASS OC 15.99940! carboxy oxygen MASS OH1 15.99940! hydroxy oxygen MASS OT 15.99940 ! TIPS3P water oxygen MASS S 32.06000! sulphur MASS SH1E 33.06800! extended atom sulfur with one hydrogen RESIdue ARG GROUp ATOM N TYPE NH1 CHARGE -0.35 END ATOM H TYPE H CHARGE 0.25 END ATOM CA TYPE CH1E CHARGE 0.10 END GROUp ATOM CB TYPE CH2E CHARGE 0.00 END ATOM CG TYPE CH2E CHARGE 0.00 END GROUp ATOM CD TYPE CH2E CHARGE 0.14 END ATOM NE TYPE NH1 CHARGE -0.35 END ATOM HE TYPE H CHARGE 0.25 END ATOM CZ TYPE C CHARGE 0.46 END GROUp ATOM NH1 TYPE NC2 CHARGE -0.25 END ATOM HH11 TYPE HC CHARGE 0.25 END ATOM HH12 TYPE HC CHARGE 0.25 END GROUp ATOM NH2 TYPE NC2 CHARGE -0.25 END ATOM HH21 TYPE HC CHARGE 0.25 END ATOM HH22 TYPE HC CHARGE 0.25 END GROUp ATOM C TYPE C CHARGE 0.45 END ATOM O TYPE O CHARGE -0.45 END BOND N CA BOND CA C BOND C O BOND N H BOND CA CB BOND CB CG BOND CG CD BOND CD NE BOND NE HE BOND NE CZ BOND CZ NH1 BOND CZ NH2 BOND NH1 HH11 BOND NH1 HH12 BOND NH2 HH21 BOND NH2 HH22 ANGLe N CA C ANGLe CA C O ANGLe H N CA ANGLe N CA CB ANGLe C CA CB ANGLe CA CB CG ANGLe CB CG CD ANGLe CG CD NE ANGLe CD NE HE ANGLe CD NE CZ ANGLe HE NE CZ ANGLe NE CZ NH1 ANGLe NE CZ NH2 ANGLe NH1 CZ NH2 ANGLe CZ NH1 HH11 ANGLe CZ NH1 HH12 ANGLe HH11 NH1 HH12 ANGLe CZ NH2 HH21 ANGLe CZ NH2 HH22 ANGLe HH21 NH2 HH22 DIHEdral N CA CB CG DIHEdral CA CB CG CD DIHEdral CB CG CD NE DIHEdral CG CD NE CZ DIHEdral CD NE CZ NH1 DIHEdral NE CZ NH1 HH11 !note: one dehidral for each hydrogen DIHEdral NE CZ NH2 HH21 ! DIHEdral NE CZ NH1 HH12 ! DIHEdral NE CZ NH2 HH22 ! IMPRoper CA N C CB !tetrahedral CA IMPRoper NE CD CZ HE !planar NE IMPRoper CZ NH1 NH2 NE !planar CZ DONOr H N DONOr HE NE DONOr HH11 NH1 DONOr HH12 NH1 DONOr HH21 NH2 DONOr HH22 NH2 ACCEptor O C END {ARG} END !TOPOLOGY {* now append another residue *} TOPOLOGY AUTOGEN ANGLE=TRUE DIHEDRAL=TRUE END RESIdue ARG2 GROUp ATOM N TYPE NH1 CHARGE -0.35 END ATOM H TYPE H CHARGE 0.25 END ATOM CA TYPE CH1E CHARGE 0.10 END GROUp ATOM CB TYPE CH2E CHARGE 0.00 END ATOM CG TYPE CH2E CHARGE 0.00 END GROUp ATOM CD TYPE CH2E CHARGE 0.14 END ATOM NE TYPE NH1 CHARGE -0.35 END ATOM HE TYPE H CHARGE 0.25 END ATOM CZ TYPE C CHARGE 0.46 END GROUp ATOM NH1 TYPE NC2 CHARGE -0.25 END ATOM HH11 TYPE HC CHARGE 0.25 END ATOM HH12 TYPE HC CHARGE 0.25 END GROUp ATOM NH2 TYPE NC2 CHARGE -0.25 END ATOM HH21 TYPE HC CHARGE 0.25 END ATOM HH22 TYPE HC CHARGE 0.25 END GROUp ATOM C TYPE C CHARGE 0.45 END ATOM O TYPE O CHARGE -0.45 END OMIT ANGLE CZ NH2 HH22 ANGLE T X Z DIHEDRAL C CA N H DIHEDRAL C CA N H OMIT DIHEDRAL H N CA CB BOND N CA BOND CA C BOND C O BOND N H BOND CA CB BOND CB CG BOND CG CD BOND CD NE BOND NE HE BOND NE CZ BOND CZ NH1 BOND CZ NH2 BOND NH1 HH11 BOND NH1 HH12 BOND NH2 HH21 BOND NH2 HH22 IMPRoper CA N C CB !tetrahedral CA IMPRoper NE CD CZ HE !planar NE IMPRoper CZ NH1 NH2 NE !planar CZ DONOr H N DONOr HE NE DONOr HH11 NH1 DONOr HH12 NH1 DONOr HH21 NH2 DONOr HH22 NH2 ACCEptor O C END {ARG} END !TOPOLOGY topology ? end STOP