XPLOR-NIH version 2.9.5 C.D. Schwieters, J.J. Kuszewski, based on X-PLOR 3.851 by A.T. Brunger N. Tjandra, and G.M. Clore J. Magn. Res., 160, 66-74 (2003). http://nmr.cit.nih.gov/xplor-nih User: [unknown] on: x86/Linux at: 04-Jun-04 10:28:03 X-PLOR>remark RTFIOTEST.INP X-PLOR>remark test the TOPOLOGY I/O X-PLOR>remark by Axel Brunger, 16-AUG-84 X-PLOR> X-PLOR>topology RTFRDR> RTFRDR>MASS H 1.00800! hydrogen which can h-bond to neutral atom RTFRDR>MASS HC 1.00800! ="= ="= ="= to charged atom RTFRDR>MASS HT 1.00800! TIPS3P water hydrogen RTFRDR>MASS C 12.01100! carbonyl carbon RTFRDR>MASS CH1E 13.01900! extended atom carbon with one hydrogen RTFRDR>MASS CH2E 14.02700! ="= ="= ="= two hydrogens RTFRDR>MASS CH3E 15.03500! ="= ="= ="= three hydrogens RTFRDR>MASS CR1E 13.01900! ="= ="= in an aromatic ring with one H RTFRDR>MASS N 14.00670! peptide nitrogen with no hydrogens attached RTFRDR>MASS NR 14.00670! nitrogen in an aromatic ring with no hydrogens RTFRDR>MASS NP 14.00670! pyrole nitrogen RTFRDR>MASS NH1 14.00670! peptide nitrogen bound to one hydrogen RTFRDR>MASS NH2 14.00670! ="= ="= ="= two hydrogens RTFRDR>MASS NH3 14.00670! nitrogen bound to three hydrogens RTFRDR>MASS NC2 14.00670! charged guandinium nitrogen bound to two hydrogens RTFRDR>MASS O 15.99940! carbonyl oxygen RTFRDR>MASS OC 15.99940! carboxy oxygen RTFRDR>MASS OH1 15.99940! hydroxy oxygen RTFRDR>MASS OT 15.99940 ! TIPS3P water oxygen RTFRDR>MASS S 32.06000! sulphur RTFRDR>MASS SH1E 33.06800! extended atom sulfur with one hydrogen RTFRDR> RTFRDR>RESIdue ARG RESIDUE> GROUp RESIDUE> ATOM N TYPE NH1 CHARGE -0.35 END RESIDUE> ATOM H TYPE H CHARGE 0.25 END RESIDUE> ATOM CA TYPE CH1E CHARGE 0.10 END RESIDUE> GROUp RESIDUE> ATOM CB TYPE CH2E CHARGE 0.00 END RESIDUE> ATOM CG TYPE CH2E CHARGE 0.00 END RESIDUE> GROUp RESIDUE> ATOM CD TYPE CH2E CHARGE 0.14 END RESIDUE> ATOM NE TYPE NH1 CHARGE -0.35 END RESIDUE> ATOM HE TYPE H CHARGE 0.25 END RESIDUE> ATOM CZ TYPE C CHARGE 0.46 END RESIDUE> GROUp RESIDUE> ATOM NH1 TYPE NC2 CHARGE -0.25 END RESIDUE> ATOM HH11 TYPE HC CHARGE 0.25 END RESIDUE> ATOM HH12 TYPE HC CHARGE 0.25 END RESIDUE> GROUp RESIDUE> ATOM NH2 TYPE NC2 CHARGE -0.25 END RESIDUE> ATOM HH21 TYPE HC CHARGE 0.25 END RESIDUE> ATOM HH22 TYPE HC CHARGE 0.25 END RESIDUE> GROUp RESIDUE> ATOM C TYPE C CHARGE 0.45 END RESIDUE> ATOM O TYPE O CHARGE -0.45 END RESIDUE> RESIDUE> BOND N CA RESIDUE> BOND CA C RESIDUE> BOND C O RESIDUE> BOND N H RESIDUE> BOND CA CB RESIDUE> BOND CB CG RESIDUE> BOND CG CD RESIDUE> BOND CD NE RESIDUE> BOND NE HE RESIDUE> BOND NE CZ RESIDUE> BOND CZ NH1 RESIDUE> BOND CZ NH2 RESIDUE> BOND NH1 HH11 RESIDUE> BOND NH1 HH12 RESIDUE> BOND NH2 HH21 RESIDUE> BOND NH2 HH22 RESIDUE> RESIDUE> ANGLe N CA C RESIDUE> ANGLe CA C O RESIDUE> ANGLe H N CA RESIDUE> ANGLe N CA CB RESIDUE> ANGLe C CA CB RESIDUE> ANGLe CA CB CG RESIDUE> ANGLe CB CG CD RESIDUE> ANGLe CG CD NE RESIDUE> ANGLe CD NE HE RESIDUE> ANGLe CD NE CZ RESIDUE> ANGLe HE NE CZ RESIDUE> ANGLe NE CZ NH1 RESIDUE> ANGLe NE CZ NH2 RESIDUE> ANGLe NH1 CZ NH2 RESIDUE> ANGLe CZ NH1 HH11 RESIDUE> ANGLe CZ NH1 HH12 RESIDUE> ANGLe HH11 NH1 HH12 RESIDUE> ANGLe CZ NH2 HH21 RESIDUE> ANGLe CZ NH2 HH22 RESIDUE> ANGLe HH21 NH2 HH22 RESIDUE> RESIDUE> DIHEdral N CA CB CG RESIDUE> DIHEdral CA CB CG CD RESIDUE> DIHEdral CB CG CD NE RESIDUE> DIHEdral CG CD NE CZ RESIDUE> DIHEdral CD NE CZ NH1 RESIDUE> DIHEdral NE CZ NH1 HH11 !note: one dehidral for each hydrogen RESIDUE> DIHEdral NE CZ NH2 HH21 ! RESIDUE> DIHEdral NE CZ NH1 HH12 ! RESIDUE> DIHEdral NE CZ NH2 HH22 ! RESIDUE> RESIDUE> IMPRoper CA N C CB !tetrahedral CA RESIDUE> IMPRoper NE CD CZ HE !planar NE RESIDUE> IMPRoper CZ NH1 NH2 NE !planar CZ RESIDUE> RESIDUE> DONOr H N RESIDUE> DONOr HE NE RESIDUE> DONOr HH11 NH1 RESIDUE> DONOr HH12 NH1 RESIDUE> DONOr HH21 NH2 RESIDUE> DONOr HH22 NH2 RESIDUE> ACCEptor O C RESIDUE> RESIDUE> IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 RESIDUE> IC N CA CB CG 0.0000 0.00 180.00 0.00 0.0000 RESIDUE> IC CA CB CG CD 0.0000 0.00 180.00 0.00 0.0000 RESIDUE> IC CB CG CD NE 0.0000 0.00 180.00 0.00 0.0000 RESIDUE> IC CG CD NE CZ 0.0000 0.00 180.00 0.00 0.0000 RESIDUE> IC CD NE CZ NH1 0.0000 0.00 180.00 0.00 0.0000 RESIDUE> IC NH1 NE *CZ NH2 0.0000 0.00 180.00 0.00 0.0000 RESIDUE> IC CD CZ *NE HE 0.0000 0.00 180.00 0.00 0.0000 RESIDUE> IC NE CZ NH1 HH11 0.0000 0.00 180.00 0.00 0.0000 RESIDUE> IC HH11 CZ *NH1 HH12 0.0000 0.00 180.00 0.00 0.0000 RESIDUE> IC NE CZ NH2 HH21 0.0000 0.00 180.00 0.00 0.0000 RESIDUE> IC HH21 CZ *NH2 HH22 0.0000 0.00 180.00 0.00 0.0000 RESIDUE> RESIDUE>END {ARG} RTFRDR> RTFRDR>END !TOPOLOGY X-PLOR> X-PLOR> X-PLOR>{* now append another residue *} X-PLOR>TOPOLOGY RTFRDR> RTFRDR>AUTOGEN AUTOGENERATE> ANGLE=TRUE AUTOGENERATE> DIHEDRAL=TRUE AUTOGENERATE>END RTFRDR> RTFRDR>RESIdue ARG2 RESIDUE> GROUp RESIDUE> ATOM N TYPE NH1 CHARGE -0.35 END RESIDUE> ATOM H TYPE H CHARGE 0.25 END RESIDUE> ATOM CA TYPE CH1E CHARGE 0.10 END RESIDUE> GROUp RESIDUE> ATOM CB TYPE CH2E CHARGE 0.00 END RESIDUE> ATOM CG TYPE CH2E CHARGE 0.00 END RESIDUE> GROUp RESIDUE> ATOM CD TYPE CH2E CHARGE 0.14 END RESIDUE> ATOM NE TYPE NH1 CHARGE -0.35 END RESIDUE> ATOM HE TYPE H CHARGE 0.25 END RESIDUE> ATOM CZ TYPE C CHARGE 0.46 END RESIDUE> GROUp RESIDUE> ATOM NH1 TYPE NC2 CHARGE -0.25 END RESIDUE> ATOM HH11 TYPE HC CHARGE 0.25 END RESIDUE> ATOM HH12 TYPE HC CHARGE 0.25 END RESIDUE> GROUp RESIDUE> ATOM NH2 TYPE NC2 CHARGE -0.25 END RESIDUE> ATOM HH21 TYPE HC CHARGE 0.25 END RESIDUE> ATOM HH22 TYPE HC CHARGE 0.25 END RESIDUE> GROUp RESIDUE> ATOM C TYPE C CHARGE 0.45 END RESIDUE> ATOM O TYPE O CHARGE -0.45 END RESIDUE> RESIDUE> OMIT ANGLE CZ NH2 HH22 RESIDUE> ANGLE T X Z RESIDUE> RESIDUE> DIHEDRAL C CA N H RESIDUE> DIHEDRAL C CA N H RESIDUE> OMIT DIHEDRAL H N CA CB RESIDUE> RESIDUE> BOND N CA RESIDUE> BOND CA C RESIDUE> BOND C O RESIDUE> BOND N H RESIDUE> BOND CA CB RESIDUE> BOND CB CG RESIDUE> BOND CG CD RESIDUE> BOND CD NE RESIDUE> BOND NE HE RESIDUE> BOND NE CZ RESIDUE> BOND CZ NH1 RESIDUE> BOND CZ NH2 RESIDUE> BOND NH1 HH11 RESIDUE> BOND NH1 HH12 RESIDUE> BOND NH2 HH21 RESIDUE> BOND NH2 HH22 RESIDUE> RESIDUE> IMPRoper CA N C CB !tetrahedral CA RESIDUE> IMPRoper NE CD CZ HE !planar NE RESIDUE> IMPRoper CZ NH1 NH2 NE !planar CZ RESIDUE> RESIDUE> DONOr H N RESIDUE> DONOr HE NE RESIDUE> DONOr HH11 NH1 RESIDUE> DONOr HH12 NH1 RESIDUE> DONOr HH21 NH2 RESIDUE> DONOr HH22 NH2 RESIDUE> ACCEptor O C RESIDUE> RESIDUE> IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 RESIDUE> IC N CA CB CG 0.0000 0.00 180.00 0.00 0.0000 RESIDUE> IC CA CB CG CD 0.0000 0.00 180.00 0.00 0.0000 RESIDUE> IC CB CG CD NE 0.0000 0.00 180.00 0.00 0.0000 RESIDUE> IC CG CD NE CZ 0.0000 0.00 180.00 0.00 0.0000 RESIDUE> IC CD NE CZ NH1 0.0000 0.00 180.00 0.00 0.0000 RESIDUE> IC NH1 NE *CZ NH2 0.0000 0.00 180.00 0.00 0.0000 RESIDUE> IC CD CZ *NE HE 0.0000 0.00 180.00 0.00 0.0000 RESIDUE> IC NE CZ NH1 HH11 0.0000 0.00 180.00 0.00 0.0000 RESIDUE> IC HH11 CZ *NH1 HH12 0.0000 0.00 180.00 0.00 0.0000 RESIDUE> IC NE CZ NH2 HH21 0.0000 0.00 180.00 0.00 0.0000 RESIDUE> IC HH21 CZ *NH2 HH22 0.0000 0.00 180.00 0.00 0.0000 RESIDUE> RESIDUE>END {ARG} RTFRDR> RTFRDR>END !TOPOLOGY X-PLOR> X-PLOR> X-PLOR>topology ? end MASS H 1.0080 MASS HC 1.0080 MASS HT 1.0080 MASS C 12.0110 MASS CH1E 13.0190 MASS CH2E 14.0270 MASS CH3E 15.0350 MASS CR1E 13.0190 MASS N 14.0067 MASS NR 14.0067 MASS NP 14.0067 MASS NH1 14.0067 MASS NH2 14.0067 MASS NH3 14.0067 MASS NC2 14.0067 MASS O 15.9994 MASS OC 15.9994 MASS OH1 15.9994 MASS OT 15.9994 MASS S 32.0600 MASS SH1E 33.0680 !----------------------------------------------------------- RESIdue ARG GROUp ATOM N TYPE=NH1 CHARge= -0.3500 MASS= 14.0067 END ATOM H TYPE=H CHARge= 0.2500 MASS= 1.0080 END ATOM CA TYPE=CH1E CHARge= 0.1000 MASS= 13.0190 END GROUp ATOM CB TYPE=CH2E CHARge= 0.0000 MASS= 14.0270 END ATOM CG TYPE=CH2E CHARge= 0.0000 MASS= 14.0270 END GROUp ATOM CD TYPE=CH2E CHARge= 0.1400 MASS= 14.0270 END ATOM NE TYPE=NH1 CHARge= -0.3500 MASS= 14.0067 END ATOM HE TYPE=H CHARge= 0.2500 MASS= 1.0080 END ATOM CZ TYPE=C CHARge= 0.4600 MASS= 12.0110 END GROUp ATOM NH1 TYPE=NC2 CHARge= -0.2500 MASS= 14.0067 END ATOM HH11 TYPE=HC CHARge= 0.2500 MASS= 1.0080 END ATOM HH12 TYPE=HC CHARge= 0.2500 MASS= 1.0080 END GROUp ATOM NH2 TYPE=NC2 CHARge= -0.2500 MASS= 14.0067 END ATOM HH21 TYPE=HC CHARge= 0.2500 MASS= 1.0080 END ATOM HH22 TYPE=HC CHARge= 0.2500 MASS= 1.0080 END GROUp ATOM C TYPE=C CHARge= 0.4500 MASS= 12.0110 END ATOM O TYPE=O CHARge= -0.4500 MASS= 15.9994 END !END GROUp 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 DIHEdral NE CZ NH2 HH21 DIHEdral NE CZ NH1 HH12 DIHEdral NE CZ NH2 HH22 IMPRoper CA N C CB IMPRoper NE CD CZ HE IMPRoper CZ NH1 NH2 NE DONOr H N DONOr HE NE DONOr HH11 NH1 DONOr HH12 NH1 DONOr HH21 NH2 DONOr HH22 NH2 ACCEptor O C IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 IC N CA CB CG 0.0000 0.00 180.00 0.00 0.0000 IC CA CB CG CD 0.0000 0.00 180.00 0.00 0.0000 IC CB CG CD NE 0.0000 0.00 180.00 0.00 0.0000 IC CG CD NE CZ 0.0000 0.00 180.00 0.00 0.0000 IC CD NE CZ NH1 0.0000 0.00 180.00 0.00 0.0000 IC NH1 NE *CZ NH2 0.0000 0.00 180.00 0.00 0.0000 IC CD CZ *NE HE 0.0000 0.00 180.00 0.00 0.0000 IC NE CZ NH1 HH11 0.0000 0.00 180.00 0.00 0.0000 IC HH11 CZ *NH1 HH12 0.0000 0.00 180.00 0.00 0.0000 IC NE CZ NH2 HH21 0.0000 0.00 180.00 0.00 0.0000 IC HH21 CZ *NH2 HH22 0.0000 0.00 180.00 0.00 0.0000 END ! RESIdue ARG !----------------------------------------------------------- RESIdue ARG2 GROUp ATOM N TYPE=NH1 CHARge= -0.3500 MASS= 14.0067 END ATOM H TYPE=H CHARge= 0.2500 MASS= 1.0080 END ATOM CA TYPE=CH1E CHARge= 0.1000 MASS= 13.0190 END GROUp ATOM CB TYPE=CH2E CHARge= 0.0000 MASS= 14.0270 END ATOM CG TYPE=CH2E CHARge= 0.0000 MASS= 14.0270 END GROUp ATOM CD TYPE=CH2E CHARge= 0.1400 MASS= 14.0270 END ATOM NE TYPE=NH1 CHARge= -0.3500 MASS= 14.0067 END ATOM HE TYPE=H CHARge= 0.2500 MASS= 1.0080 END ATOM CZ TYPE=C CHARge= 0.4600 MASS= 12.0110 END GROUp ATOM NH1 TYPE=NC2 CHARge= -0.2500 MASS= 14.0067 END ATOM HH11 TYPE=HC CHARge= 0.2500 MASS= 1.0080 END ATOM HH12 TYPE=HC CHARge= 0.2500 MASS= 1.0080 END GROUp ATOM NH2 TYPE=NC2 CHARge= -0.2500 MASS= 14.0067 END ATOM HH21 TYPE=HC CHARge= 0.2500 MASS= 1.0080 END ATOM HH22 TYPE=HC CHARge= 0.2500 MASS= 1.0080 END GROUp ATOM C TYPE=C CHARge= 0.4500 MASS= 12.0110 END ATOM O TYPE=O CHARge= -0.4500 MASS= 15.9994 END !END GROUp 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 T X Z ANGLe N CA C ANGLe CA N H ANGLe N CA CB ANGLe CA C O 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 CZ NH2 HH21 ANGLe HH11 NH1 HH12 ANGLe HH21 NH2 HH22 DIHEdral C CA N H DIHEdral C CA N H DIHEdral N CA C O DIHEdral O C CA CB DIHEdral N CA CB CG DIHEdral C CA CB CG DIHEdral CA CB CG CD DIHEdral CB CG CD NE DIHEdral CG CD NE HE DIHEdral CG CD NE CZ DIHEdral CD NE CZ NH1 DIHEdral CD NE CZ NH2 DIHEdral HE NE CZ NH1 DIHEdral HE NE CZ NH2 DIHEdral NE CZ NH1 HH11 DIHEdral NE CZ NH1 HH12 DIHEdral NH2 CZ NH1 HH11 DIHEdral NH2 CZ NH1 HH12 DIHEdral NE CZ NH2 HH21 DIHEdral NE CZ NH2 HH22 DIHEdral NH1 CZ NH2 HH21 DIHEdral NH1 CZ NH2 HH22 IMPRoper CA N C CB IMPRoper NE CD CZ HE IMPRoper CZ NH1 NH2 NE DONOr H N DONOr HE NE DONOr HH11 NH1 DONOr HH12 NH1 DONOr HH21 NH2 DONOr HH22 NH2 ACCEptor O C IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 IC N CA CB CG 0.0000 0.00 180.00 0.00 0.0000 IC CA CB CG CD 0.0000 0.00 180.00 0.00 0.0000 IC CB CG CD NE 0.0000 0.00 180.00 0.00 0.0000 IC CG CD NE CZ 0.0000 0.00 180.00 0.00 0.0000 IC CD NE CZ NH1 0.0000 0.00 180.00 0.00 0.0000 IC NH1 NE *CZ NH2 0.0000 0.00 180.00 0.00 0.0000 IC CD CZ *NE HE 0.0000 0.00 180.00 0.00 0.0000 IC NE CZ NH1 HH11 0.0000 0.00 180.00 0.00 0.0000 IC HH11 CZ *NH1 HH12 0.0000 0.00 180.00 0.00 0.0000 IC NE CZ NH2 HH21 0.0000 0.00 180.00 0.00 0.0000 IC HH21 CZ *NH2 HH22 0.0000 0.00 180.00 0.00 0.0000 END ! RESIdue ARG2 X-PLOR> X-PLOR>STOP HEAP: maximum use= 862135 current use= 846467 X-PLOR: total CPU time= 0.1600 s X-PLOR: entry time at 10:28:03 04-Jun-04 X-PLOR: exit time at 10:28:03 04-Jun-04