REMARKS TOPH11.PRO ( from TOPH10.INP) REMARKS ============================= REMARKS Charges and atom order modified for neutral GROUPs. REMARKS Histidine charges set to Del Bene and Cohen sto-3g calculations. REMARKS Amide charges set to match the experimental dipole moment. REMARKS DNA/RNA atoms appended . REMARKS few atoms never referenced switched off. REMARKS Default for HIStidines is the doubly protonated state set echo=false end AUTOGENERATE ANGLES=TRUE END {*===========================*} {* protein default masses *} MASS H 1.00800! hydrogen which can h-bond to neutral atom MASS HC 1.00800! ="= ="= ="= to charged atom !MASS HA 1.00800! aliphatic hydrogen !MASS CT 12.01100! aliphatic carbon 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 S 32.06000! sulphur MASS SH1E 33.06800! extended atom sulfur with one hydrogen !some empirical rules for the following topologies: ! ! 1. angles are taken between all permutations of atoms bonded to ! a particular atom. Exception: 2 angles linking the THR double ring ! 2. each bond with non-terminal atoms creates one dihedral. Exception: ! ring bonds in aromatic side chains (but not PRO). ! 3. each planar atom vertex creates one improper-planar term ! execption: ARG head groups. ! 4. each 1-extended-H carbon atom creates one improper-tetrahedral term ! (for chirality) ! 5. Each bond in an aromatic ring creates one improper-torsion term ! (exception: PRO) ! 6. LYS head groups and methyl head groups create one dihedral for ! each hydrogen ! 7. all 1:2 and 1:3 nonbonded interactions are assumed to be excluded ! 8. All 1:4,1:5,... non-bonded interactions in aromatic rings ! (or double rings) are explicitly excluded ! ! --------------------------------------------------------------------- RESIdue ALA 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=CH3E CHARge= 0.00 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 IMPRoper CA N C CB !tetrahedral CA DONOr H N ACCEptor O C IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 END {ALA} !------------------------------------------------------------------ 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 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 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 {ARG} !------------------------------------------------------------------ RESIdue ASN 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 GROUp ATOM CG TYPE=C CHARge= 0.45 END ATOM OD1 TYPE=O CHARge=-0.45 END GROUp ATOM ND2 TYPE=NH2 CHARge=-0.50 END ATOM HD21 TYPE=H CHARge= 0.25 END ATOM HD22 TYPE=H 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 OD1 BOND CG ND2 BOND ND2 HD21 BOND ND2 HD22 DIHEdral N CA CB CG DIHEdral CA CB CG OD1 DIHEdral CB CG ND2 HD21 IMPRoper CA N C CB !tetrahedral CA IMPRoper CG OD1 ND2 CB !planar CG IMPRoper ND2 HD21 HD22 CG !planar ND2 DONOr H N DONOr HD21 ND2 DONOr HD22 ND2 ACCEptor OD1 CG 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 OD1 0.0000 0.00 180.00 0.00 0.0000 IC OD1 CB *CG ND2 0.0000 0.00 180.00 0.00 0.0000 IC OD1 CG ND2 HD21 0.0000 0.00 180.00 0.00 0.0000 IC HD21 CG *ND2 HD22 0.0000 0.00 180.00 0.00 0.0000 END {ASN} !------------------------------------------------------------------ RESIdue ASP 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=-0.16 END ATOM CG TYPE=C CHARge= 0.36 END ATOM OD1 TYPE=OC CHARge=-0.60 END ATOM OD2 TYPE=OC CHARge=-0.60 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 OD1 BOND CG OD2 DIHEdral N CA CB CG DIHEdral CA CB CG OD1 IMPRoper CA N C CB !tetrahedral CA IMPRoper CG OD1 OD2 CB !planar CG DONOr H N ACCEptor OD1 CG ACCEptor OD2 CG 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 OD1 0.0000 0.00 180.00 0.00 0.0000 IC OD1 CB *CG OD2 0.0000 0.00 180.00 0.00 0.0000 END {ASP} !------------------------------------------------------------------ RESIdue CYS 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= 0.19 END ATOM SG TYPE=SH1E CHARge=-0.19 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 SG DIHEdral N CA CB SG IMPRoper CA N C CB !tetrahedral CA DONOr H N ACCEptor O C IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 IC N CA CB SG 0.0000 0.00 180.00 0.00 0.0000 END {CYS} !------------------------------------------------------------------ RESIdue GLN 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=C CHARge= 0.45 END ATOM OE1 TYPE=O CHARge=-0.45 END GROUp ATOM NE2 TYPE=NH2 CHARge=-0.50 END ATOM HE21 TYPE=H CHARge= 0.25 END ATOM HE22 TYPE=H 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 OE1 BOND CD NE2 BOND NE2 HE21 BOND NE2 HE22 DIHEdral N CA CB CG DIHEdral CA CB CG CD DIHEdral CB CG CD OE1 DIHEdral CG CD NE2 HE21 IMPRoper CA N C CB !tetrahedral CA IMPRoper CD OE1 NE2 CG !planar CD IMPRoper NE2 HE21 HE22 CD !planar NE2 DONOr H N DONOr HE21 NE2 DONOr HE22 NE2 ACCEptor OE1 CD 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 OE1 0.0000 0.00 180.00 0.00 0.0000 IC OE1 CG *CD NE2 0.0000 0.00 180.00 0.00 0.0000 IC OE1 CD NE2 HE21 0.0000 0.00 180.00 0.00 0.0000 IC HE21 CD *NE2 HE22 0.0000 0.00 180.00 0.00 0.0000 END {GLN} !------------------------------------------------------------------ RESIdue GLU 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 GROUp ATOM CG TYPE=CH2E CHARge=-0.16 END ATOM CD TYPE=C CHARge= 0.36 END ATOM OE1 TYPE=OC CHARge=-0.60 END ATOM OE2 TYPE=OC CHARge=-0.60 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 OE1 BOND CD OE2 DIHEdral N CA CB CG DIHEdral CA CB CG CD DIHEdral CB CG CD OE1 !note: only one dihedral for CG-CD IMPRoper CA N C CB !tetrahedral CA IMPRoper CD OE1 OE2 CG !planar CD DONOr H N ACCEptor OE1 CD ACCEptor OE2 CD 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 OE1 0.0000 0.00 180.00 0.00 0.0000 IC OE1 CG *CD OE2 0.0000 0.00 180.00 0.00 0.0000 END {GLU} !------------------------------------------------------------------ RESIdue GLY GROUp ATOM N TYPE=NH1 CHARge=-0.35 END ATOM H TYPE=H CHARge= 0.25 END ATOM CA TYPE=CH2E CHARge= 0.10 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 DONOr H N ACCEptor O C END {GLY} !------------------------------------------------------------------ RESIdue HIS { Doubly protonated histidine. Ring charges Hayes and Kollman jacs 98:3335 (1976) } 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= 0.10 END ATOM CG TYPE=C CHARge= 0.15 END ATOM CD2 TYPE=CR1E CHARge= 0.20 END GROUp ATOM ND1 TYPE=NH1 CHARge=-0.25 END ATOM HD1 TYPE=H CHARge= 0.32 END GROUp ATOM CE1 TYPE=CR1E CHARge= 0.41 END GROUp ATOM NE2 TYPE=NH1 CHARge=-0.25 END ATOM HE2 TYPE=H CHARge= 0.32 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 ND1 BOND CG CD2 BOND ND1 HD1 BOND ND1 CE1 BOND CD2 NE2 BOND CE1 NE2 BOND NE2 HE2 DIHEdral N CA CB CG DIHEdral CA CB CG ND1 IMPRoper CA N C CB !tetrahedral CA IMPRoper CG ND1 CD2 CB !planar CG IMPRoper ND1 CG CE1 HD1 !planar ND1 IMPRoper NE2 CD2 CE1 HE2 !planar NE2 IMPRoper CG ND1 CE1 NE2 !! IMPRoper ND1 CE1 NE2 CD2 !! IMPRoper CE1 NE2 CD2 CG !! ring torsions IMPRoper NE2 CD2 CG ND1 !! IMPRoper CD2 CG ND1 CE1 !! DONOr H N DONOr HD1 ND1 DONOr HE2 NE2 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 CD2 0.0000 0.00 90.00 0.00 0.0000 IC CD2 CB *CG ND1 0.0000 0.00 180.00 0.00 0.0000 IC CD2 CG ND1 CE1 0.0000 0.00 0.00 0.00 0.0000 IC ND1 CG CD2 NE2 0.0000 0.00 0.00 0.00 0.0000 IC CE1 CG *ND1 HD1 0.0000 0.00 180.00 0.00 0.0000 IC CE1 CD2 *NE2 HE2 0.0000 0.00 180.00 0.00 0.0000 END {HIS} !------------------------------------------------------------------ RESIdue ILE 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=CH1E CHARge= 0.00 END ATOM CG2 TYPE=CH3E CHARge= 0.00 END GROUp ATOM CG1 TYPE=CH2E CHARge= 0.00 END ATOM CD TYPE=CH3E CHARge= 0.00 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 CG1 BOND CB CG2 BOND CG1 CD DIHEdral N CA CB CG1 !note: only one dihedral around CA-CB DIHEdral CA CB CG1 CD IMPRoper CA N C CB !tetrahedral CA IMPRoper CB CG1 CG2 CA !planar CB DONOr H N ACCEptor O C IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 IC N CA CB CG1 0.0000 0.00 180.00 0.00 0.0000 IC CA CB CG1 CD 0.0000 0.00 180.00 0.00 0.0000 IC CG1 CA *CB CG2 0.0000 0.00 -120.00 0.00 0.0000 END {ILE} !------------------------------------------------------------------ RESIdue LEU 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=CH1E CHARge= 0.00 END ATOM CD1 TYPE=CH3E CHARge= 0.00 END ATOM CD2 TYPE=CH3E CHARge= 0.00 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 CD1 BOND CG CD2 DIHEdral N CA CB CG DIHEdral CA CB CG CD2 !note: only one dihedral around CB-CG IMPRoper CA N C CB !tetrahedral CA IMPRoper CG CD2 CD1 CB !planar CG DONOr H N 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 CD1 0.0000 0.00 180.00 0.00 0.0000 IC CD1 CB *CG CD2 0.0000 0.00 120.00 0.00 0.0000 END {LEU} !------------------------------------------------------------------ RESIdue LYS 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 ATOM CD TYPE=CH2E CHARge= 0.00 END GROUp ATOM CE TYPE=CH2E CHARge= 0.22 END ATOM NZ TYPE=NH3 CHARge= 0.00 END ATOM HZ1 TYPE=HC CHARge= 0.26 END ATOM HZ2 TYPE=HC CHARge= 0.26 END ATOM HZ3 TYPE=HC CHARge= 0.26 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 CE BOND CE NZ BOND NZ HZ1 BOND NZ HZ2 BOND NZ HZ3 DIHEdral N CA CB CG DIHEdral CA CB CG CD DIHEdral CB CG CD CE DIHEdral CG CD CE NZ DIHEdral CD CE NZ HZ1 !! DIHEdral CD CE NZ HZ2 !!note: dihedrals for each hydrogen DIHEdral CD CE NZ HZ3 !! IMPRoper CA N C CB !tetrahedral CA DONOr H N DONOr HZ1 NZ DONOr HZ2 NZ DONOr HZ3 NZ 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 CE 0.0000 0.00 180.00 0.00 0.0000 IC CG CD CE NZ 0.0000 0.00 180.00 0.00 0.0000 IC CD CE NZ HZ1 0.0000 0.00 180.00 0.00 0.0000 IC HZ1 CE *NZ HZ2 0.0000 0.00 120.00 0.00 0.0000 IC HZ2 CE *NZ HZ3 0.0000 0.00 120.00 0.00 0.0000 END {LYS} !------------------------------------------------------------------ RESIdue MET 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 GROUp ATOM CG TYPE=CH2E CHARge= 0.06 END ATOM SD TYPE=S CHARge=-0.12 END ATOM CE TYPE=CH3E CHARge= 0.06 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 SD BOND SD CE DIHEdral N CA CB CG DIHEdral CA CB CG SD DIHEdral CB CG SD CE IMPRoper CA N C CB !tetrahedral CA DONOr H N 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 SD 0.0000 0.00 180.00 0.00 0.0000 IC CB CG SD CE 0.0000 0.00 180.00 0.00 0.0000 END {MET} !------------------------------------------------------------------ RESIdue PHE 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=C CHARge= 0.00 EXCLusion=( CZ ) END ATOM CD1 TYPE=CR1E CHARge= 0.00 EXCLusion=( CE2 ) END ATOM CD2 TYPE=CR1E CHARge= 0.00 EXCLusion=( CE1 ) END GROUp ATOM CE1 TYPE=CR1E CHARge= 0.00 END ATOM CE2 TYPE=CR1E CHARge= 0.00 END ATOM CZ TYPE=CR1E CHARge= 0.00 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 CD1 BOND CG CD2 BOND CD1 CE1 BOND CD2 CE2 BOND CE1 CZ BOND CE2 CZ DIHEdral N CA CB CG DIHEdral CA CB CG CD1 !note: only one dihedral around CB-CG IMPRoper CA N C CB !tetrahedral CA IMPRoper CG CD1 CD2 CB !planar CG IMPRoper CG CD1 CE1 CZ !! IMPRoper CD1 CE1 CZ CE2 !! IMPRoper CE1 CZ CE2 CD2 !! ring torsions IMPRoper CZ CE2 CD2 CG !! IMPRoper CE2 CD2 CG CD1 !! IMPRoper CD2 CG CD1 CE1 !! DONOr H N 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 CD1 0.0000 0.00 90.00 0.00 0.0000 IC CD1 CB *CG CD2 0.0000 0.00 180.00 0.00 0.0000 IC CD1 CG CD2 CE2 0.0000 0.00 0.00 0.00 0.0000 IC CD2 CG CD1 CE1 0.0000 0.00 0.00 0.00 0.0000 IC CG CD1 CE1 CZ 0.0000 0.00 0.00 0.00 0.0000 END {PHE} !------------------------------------------------------------------ RESIdue PRO GROUp ATOM N TYPE=N CHARge=-0.20 END ATOM CD TYPE=CH2E CHARge= 0.10 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 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 CD BOND CA CB BOND CB CG BOND CG CD DIHEdral N CA CB CG !! DIHEdral CA CB CG CD !! DIHEdral CB CG CD N !! the PROline ring is represented by dihedrals DIHEdral CG CD N CA !! IMPRoper CA N C CB !tetrahedral CA 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 0.00 0.00 0.0000 END {PRO} !------------------------------------------------------------------ RESIdue SER 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= 0.15 END ATOM OG TYPE=OH1 CHARge=-0.40 END ATOM HG TYPE=H 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 OG BOND OG HG DIHEdral N CA CB OG DIHEdral CA CB OG HG IMPRoper CA N C CB !tetrahedral CA DONOr H N DONOr HG OG ACCEptor OG " " ACCEptor O C IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 IC N CA CB OG 0.0000 0.00 180.00 0.00 0.0000 IC CA CB OG HG 0.0000 0.00 180.00 0.00 0.0000 END {SER} !------------------------------------------------------------------ RESIdue THR 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=CH1E CHARge= 0.15 END ATOM OG1 TYPE=OH1 CHARge=-0.40 END ATOM HG1 TYPE=H CHARge= 0.25 END GROUp ATOM CG2 TYPE=CH3E CHARge= 0.00 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 OG1 BOND CB CG2 BOND OG1 HG1 DIHEdral N CA CB OG1 !note: only one dihedral around CA-CB DIHEdral CA CB OG1 HG1 IMPRoper CA N C CB !tetrahedral CA IMPRoper CB OG1 CG2 CA !planar CB DONOr H N DONOr HG1 OG1 ACCEptor OG1 " " ACCEptor O C IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 IC N CA CB OG1 0.0000 0.00 180.00 0.00 0.0000 IC OG1 CA *CB CG2 0.0000 0.00 -120.00 0.00 0.0000 IC CA CB OG1 HG1 0.0000 0.00 180.00 0.00 0.0000 END {THR} !------------------------------------------------------------------ RESIdue TRP 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 GROUp ATOM CG TYPE=C CHARge=-0.03 EXCL=(CD1 CD2 NE1 CE2 CE3 CZ2 CZ3 CH2) END ATOM CD2 TYPE=C CHARge= 0.10 EXCL=(NE1 CE2 CE3 CZ2 CZ3 CH2) END ATOM CE2 TYPE=C CHARge=-0.04 EXCL=(CE3 CZ2 CZ3 CH2) END ATOM CE3 TYPE=CR1E CHARge=-0.03 EXCL=(CZ2 CZ3 CH2) END GROUp ATOM CD1 TYPE=CR1E CHARge= 0.06 EXCL=(CD2 NE1 CE2 CE3 CZ2 CZ3 CH2) END ATOM NE1 TYPE=NH1 CHARge=-0.26 EXCL=(CE2 CE3 CZ2 CZ3 CH2) END ATOM HE1 TYPE=H CHARge= 0.20 END GROUp ATOM CZ2 TYPE=CR1E CHARge= 0.00 EXCL=(CZ3 CH2) END ATOM CZ3 TYPE=CR1E CHARge= 0.00 EXCL=(CH2) END ATOM CH2 TYPE=CR1E CHARge= 0.00 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 CD1 BOND CG CD2 BOND CD1 NE1 BOND CD2 CE2 BOND NE1 HE1 BOND NE1 CE2 BOND CD2 CE3 BOND CE2 CZ2 BOND CE3 CZ3 BOND CZ2 CH2 BOND CZ3 CH2 OMIT ANGLe CG CD2 CE3 OMIT ANGLe NE1 CE2 CZ2 ! The ring angles are only assigned for the five and six member rings. ! The angles CG CD2 CE3 and NE1 CE2 CZ2 are left out to avoid conflicts ! with the histidine angle parameters and to preserve symmetry. DIHEdral N CA CB CG DIHEdral CA CB CG CD1 DIHEdral CD1 CE2 CD2 CZ3 !! DIHEdral CD1 CD2 CE2 CH2 !! these dihedrals span the rings and keep DIHEdral CZ2 CE2 CD2 CG !! them parallel DIHEdral CE3 CD2 CE2 NE1 !! IMPRoper CA N C CB !tetrahedral CA IMPRoper CG CD1 CD2 CB !planar CG IMPRoper NE1 CD1 CE2 HE1 !planar NE1 IMPRoper CD2 CE2 CZ2 CH2 !! IMPRoper CE2 CZ2 CH2 CZ3 !! IMPRoper CZ2 CH2 CZ3 CE3 !! torsions ring 2 IMPRoper CH2 CZ3 CE3 CD2 !! IMPRoper CZ3 CE3 CD2 CE2 !! IMPRoper CE3 CD2 CE2 CZ2 !! IMPRoper CG CD1 NE1 CE2 !! IMPRoper CD1 NE1 CE2 CD2 !! IMPRoper NE1 CE2 CD2 CG !! torsions ring 1 IMPRoper CE2 CD2 CG CD1 !! IMPRoper CD2 CG CD1 NE1 !! DONOr H N DONOr HE1 NE1 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 CD2 0.0000 0.00 180.00 0.00 0.0000 IC CD2 CB *CG CD1 0.0000 0.00 180.00 0.00 0.0000 IC CD1 CG CD2 CE2 0.0000 0.00 0.00 0.00 0.0000 IC CD2 CG CD1 NE1 0.0000 0.00 0.00 0.00 0.0000 IC CE2 CD1 *NE1 HE1 0.0000 0.00 180.00 0.00 0.0000 IC CE2 CG *CD2 CE3 0.0000 0.00 180.00 0.00 0.0000 IC CE2 CD2 CE3 CZ3 0.0000 0.00 0.00 0.00 0.0000 IC CE3 CD2 CE2 CZ2 0.0000 0.00 0.00 0.00 0.0000 IC CD2 CE2 CZ2 CH2 0.0000 0.00 0.00 0.00 0.0000 END {THR} !------------------------------------------------------------------ RESIdue TYR 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=C CHARge= 0.00 EXCLusion=( CZ ) END GROUp ATOM CD1 TYPE=CR1E CHARge= 0.00 EXCLusion=( CE2 ) END ATOM CE1 TYPE=CR1E CHARge= 0.00 EXCLusion=( CD2 ) END GROUp ATOM CD2 TYPE=CR1E CHARge= 0.00 END ATOM CE2 TYPE=CR1E CHARge= 0.00 END GROUp ATOM CZ TYPE=C CHARge= 0.15 END ATOM OH TYPE=OH1 CHARge=-0.40 END ATOM HH TYPE=H 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 CD1 BOND CG CD2 BOND CD1 CE1 BOND CD2 CE2 BOND CE1 CZ BOND CE2 CZ BOND CZ OH BOND OH HH DIHEdral N CA CB CG DIHEdral CA CB CG CD1 DIHEdral CE2 CZ OH HH IMPRoper CA N C CB !tetrahedral CA IMPRoper CG CD1 CD2 CB !planar CG IMPRoper CZ CE1 CE2 OH !planar CZ IMPRoper CG CD1 CE1 CZ !! IMPRoper CD1 CE1 CZ CE2 !! IMPRoper CE1 CZ CE2 CD2 !! ring torsions IMPRoper CZ CE2 CD2 CG !! IMPRoper CE2 CD2 CG CD1 !! IMPRoper CD2 CG CD1 CE1 !! DONOr H N DONOr HH OH ACCEptor OH " " 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 CD1 0.0000 0.00 90.00 0.00 0.0000 IC CD1 CB *CG CD2 0.0000 0.00 180.00 0.00 0.0000 IC CD2 CG CD1 CE1 0.0000 0.00 0.00 0.00 0.0000 IC CD1 CG CD2 CE2 0.0000 0.00 0.00 0.00 0.0000 IC CG CD1 CE1 CZ 0.0000 0.00 0.00 0.00 0.0000 IC CE2 CE1 *CZ OH 0.0000 0.00 180.00 0.00 0.0000 IC CE1 CZ OH HH 0.0000 0.00 180.00 0.00 0.0000 END {TYR} !------------------------------------------------------------------ RESIdue VAL 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=CH1E CHARge= 0.00 END ATOM CG1 TYPE=CH3E CHARge= 0.00 END ATOM CG2 TYPE=CH3E CHARge= 0.00 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 CG1 BOND CB CG2 DIHEdral N CA CB CG1 !note: only one dihedral around CA-CB IMPRoper CA N C CB !tetrahedral CA IMPRoper CB CG2 CG1 CA !planar CB DONOr H N ACCEptor O C IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 IC N CA CB CG1 0.0000 0.00 180.00 0.00 0.0000 IC CG1 CA *CB CG2 0.0000 0.00 120.00 0.00 0.0000 END {VAL} !------------------------------------------------------------------ RESIdue ACE { Acetyl blocking GROUp with standard naming. can be linked: ACE * \ PEPT / } GROUp ATOM CA TYPE=CH3E CHARge= 0.00 END GROUp ATOM C TYPE=C CHARge= 0.45 END ATOM O TYPE=O CHARge=-0.45 END BOND CA C BOND C O ACCEptor O C END {ACE} !------------------------------------------------------------------ RESIdue CBX { can be linked * CBX \PEPT/ } GROUp ATOM N TYPE=NH1 CHARge=-0.35 END ATOM H TYPE=H CHARge= 0.25 END ATOM CA TYPE=CH3E CHARge= 0.10 END BOND N CA BOND N H DONOr H N END {CBX} !---------------------------------------------------------------------- RESIdue ETH GROUp ATOM C2 TYPE=CH3E CHARge= 0.00 END GROUp ATOM C1 TYPE=CH2E CHARge= 0.15 END ATOM O TYPE=OH1 CHARge=-0.40 END ATOM H TYPE=H CHARge= 0.25 END BOND C2 C1 BOND C1 O BOND O H DIHEdral C2 C1 O H DONOr H O ACCEptor O " " END {ETH} !------------------------------------------------------------------ RESIdue SO4 { sulfate group } GROUp ATOM S TYPE=S CHARge= 0.0 END ATOM O1 TYPE=OC CHARge=-0.5 END ATOM O2 TYPE=OC CHARge=-0.5 END ATOM O3 TYPE=OC CHARge=-0.5 END ATOM O4 TYPE=OC CHARge=-0.5 END BOND S O1 BOND S O2 BOND S O3 BOND S O4 ACCEptor O1 S ACCEptor O2 S ACCEptor O3 S ACCEptor O4 S END {SO4} !------------------------------------------------------------------ PRESidue DISU { disulfide bridge ...CYS CYS... \DISU/ } GROUP MODIfy ATOM 1CB CHARge= 0.19 END MODIfy ATOM 1SG TYPE=S CHARge=-0.19 END GROUP MODIfy ATOM 2CB CHARge= 0.19 END MODIfy ATOM 2SG TYPE=S CHARge=-0.19 END ADD BOND 1SG 2SG ADD ANGLe 1CB 1SG 2SG ADD ANGLe 1SG 2SG 2CB ADD DIHEdral 1CA 1CB 1SG 2SG ADD DIHEdral 1CB 1SG 2SG 2CB ADD DIHEdral 1SG 2SG 2CB 2CA ADD IC 1CA 1CB 1SG 2SG 0.0 0.0 180.0 0.0 0.0 ADD IC 1CB 1SG 2SG 2CB 0.0 0.0 180.0 0.0 0.0 ADD IC 1SG 2SG 2CB 2CA 0.0 0.0 180.0 0.0 0.0 END {DISU} !---------------------------------------------------------------------- PRESidue PEPT { PEPTide bond link, for all amino acids ...*(-) (+)*... \ PEPT / except the *(-) - (+)PRO link } ADD BOND -C +N ADD ANGLE -CA -C +N ADD ANGLE -O -C +N ADD ANGLE -C +N +CA ADD ANGLE -C +N +H ADD DIHEdral -C +N +CA +C ADD DIHEdral -N -CA -C +N ADD DIHEdral -CA -C +N +CA ADD IMPRoper -C -CA +N -O {planar -C} ADD IMPRoper +N -C +CA +H {planar +N} ADD IC -C +CA *+N +H 0.0 0.0 180.0 0.0 0.0 ! planar -C ADD IC -C +N +CA +C 0.0 0.0 180.0 0.0 0.0 ADD IC -N -CA -C +N 0.0 0.0 180.0 0.0 0.0 ADD IC -CA -C +N +CA 0.0 0.0 180.0 0.0 0.0 ADD IC +N -CA *-C -O 0.0 0.0 180.0 0.0 0.0 ! planar +N END {PEPT} !---------------------------------------------------------------------- PRESidue PEPP { for ...*(-) - (+)PRO link same as PEPT except replacement H by CD and improper +N +CA +CD -C } ADD BOND -C +N ADD ANGLE -CA -C +N ADD ANGLE -O -C +N ADD ANGLE -C +N +CA ADD ANGLE -C +N +CD ADD DIHEdral -C +N +CA +C ADD DIHEdral -N -CA -C +N ADD DIHEdral -CA -C +N +CA ADD IMPRoper -C -CA +N -O {planar -C} ADD IMPRoper +N +CA +CD -C {planar +N} ADD IC -C +CA *+N +CD 0.0 0.0 180.0 0.0 0.0 ! planar +N ADD IC -C +N +CA +C 0.0 0.0 180.0 0.0 0.0 ADD IC -N -CA -C +N 0.0 0.0 180.0 0.0 0.0 ADD IC -CA -C +N +CA 0.0 0.0 180.0 0.0 0.0 ADD IC +N -CA *-C -O 0.0 0.0 180.0 0.0 0.0 ! planar -C END {PEPP} !------------------------------------------------------------------ PRESidue NTER { can be patched ( as NTER - * ... ) to any amino acid except PRO } GROUp ADD ATOM +HT1 TYPE=HC CHARge=0.26 END ADD ATOM +HT2 TYPE=HC CHARge=0.26 END MODIfy ATOM +N TYPE=NH3 CHARge=0.00 END ADD ATOM +HT3 TYPE=HC CHARge=0.26 END DELETE ATOM +H END MODIfy ATOM +CA CHARge=0.22 END ADD BOND +HT1 +N ADD BOND +HT2 +N ADD BOND +HT3 +N ADD ANGLe +HT1 +N +HT2 ADD ANGLe +HT2 +N +HT3 ADD ANGLe +HT2 +N +CA ADD ANGLe +HT1 +N +HT3 ADD ANGLe +HT1 +N +CA ADD ANGLe +HT3 +N +CA ADD DIHEdral +HT2 +N +CA +C ADD DIHEdral +HT1 +N +CA +C ADD DIHEdral +HT3 +N +CA +C ADD DONOr +HT1 +N ADD DONOr +HT2 +N ADD DONOr +HT3 +N ADD IC +HT1 +N +CA +C 0.0000 0.00 180.00 0.00 0.0000 ADD IC +HT2 +CA *+N +HT1 0.0000 0.00 120.00 0.00 0.0000 ADD IC +HT3 +CA *+N +HT2 0.0000 0.00 120.00 0.00 0.0000 END {NTER} !------------------------------------------------------------------ PRESidue PROP { this is the N-terminal for PROlines PROP - PRO -... } GROUp ADD ATOM +HT1 TYPE=HC CHARge= 0.26 END ADD ATOM +HT2 TYPE=HC CHARge= 0.26 END MODIfy ATOM +N TYPE=NH3 CHARge= 0.08 END MODIfy ATOM +CD CHARge= 0.20 END MODIfy ATOM +CA CHARge= 0.20 END ADD BOND +HT1 +N ADD BOND +HT2 +N ADD ANGLe +HT1 +N +HT2 ADD ANGLe +HT2 +N +CA ADD ANGLe +HT1 +N +CD ADD ANGLe +HT1 +N +CA ADD ANGLe +CD +N +HT2 ADD DIHEdral +HT2 +N +CA +C ADD DIHEdral +HT1 +N +CA +C ADD DONOr +HT1 +N ADD DONOr +HT2 +N ADD IC +HT1 +CA *+N +CD 0.0000 0.00 120.00 0.00 0.0000 ADD IC +HT2 +CA *+N +HT1 0.0000 0.00 120.00 0.00 0.0000 END {PROP} !------------------------------------------------------------------ PRESidue CTER { C-terminal for all amino acids ... * - CTER } GROUp MODIfy ATOM -C CHARge= 0.14 END ADD ATOM -OT1 TYPE=OC CHARge=-0.57 END ADD ATOM -OT2 TYPE=OC CHARge=-0.57 END DELETE ATOM -O END ADD BOND -C -OT1 ADD BOND -C -OT2 ADD ANGLe -CA -C -OT1 ADD ANGLe -CA -C -OT2 ADD ANGLe -OT1 -C -OT2 ADD DIHEdral -N -CA -C -OT2 ADD IMPRoper -C -CA -OT2 -OT1 ADD ACCEptor -OT1 -C ADD ACCEptor -OT2 -C ADD IC -N -CA -C -OT2 0.0 0.0 180.0 0.0 0.0 ADD IC -OT2 -CA *-C -OT1 0.0 0.0 180.0 0.0 0.0 END {CTER} !------------------------------------------------------------------ set echo=true end