remark file parallhdg.pro version 4.01 date 29-Jul-96 remark file topallhdg.pro version 4.01 date 29-Jul-96 remark Geometric energy function parameters for distance geometry and remark simulated annealing. remark Author: Michael Nilges, EMBL Heidelberg !set echo off message off end !***********************************************************************! ! Copyright (C) 1995,1996 by Michael Nilges. All rights reserved. ! ! Copying and redistribution of this files is authorized only if etiher ! ! (1) you make absolutely no changes to your copy, including name, or ! ! (2) if you do make changes, you name it something other than ! ! topallhdg.pro and topallhdg.x.xx.pro, and clearly mark the changes. ! ! The information in this software is subject to change without notice ! ! and should not be construed as a commitment by the EMBL or by the ! ! authors. Neither the EMBL, Yale University, nor the authors assume ! ! responsibility for the use or reliability of this software. ! ! We do hope, however, to get responses from users, especially when ! ! errors have been found. ! !***********************************************************************! ! Description: ! ! This parameter file was originally derived from the CHARMM parameter ! ! file PARMALLH6. It was designed specifically for the initial stages ! ! of calculating structures from NMR restraints. ! !***********************************************************************! ! History: ! version 4.02 (17-DEC-97) : Histidine hbond acceptor/donor corrected ! version 4.01 (29-Jul-96) : all covalent parameters ! version 4.00 (19-Jul-96) : all atom types from CSDX implemented ! version 3.00 (24-Oct-95) : mapped CSDX parmameters on parallhdg, ! no changes in topallhdg ! previous modifications: ! proline residue modified, puckering enforced (MN) ! added hbond acceptor and donor definitions for analysis (MN) ! all references to internal coordinates (IC's) removed (MN) ! added stereospecific impropers for all pro-chiral centers (ATB, JK) ! all dihedrals defining planarity converted to impropers (MN, PK) ! additional impropers at planar centers (MN) !***********************************************************************! !set message off echo off end autogenerate angles=true dihedrals=false end mass H 1.008 mass HC 1.008 mass HA 1.008 mass C 12.011 mass CH1E 12.011 mass CH2E 12.011 mass CH3E 12.011 mass CH2G 12.011 mass CH2P 12.011 mass C5W 12.011 mass CW 12.011 mass CR1E 12.011 mass C5 12.011 mass CRH 12.011 mass CR1H 12.011 mass CR1W 12.011 mass CRHH 12.011 mass CF 12.011 mass CY 12.011 mass CY2 12.011 mass N 14.007 mass NR 14.007 mass NH1 14.007 mass NH2 14.007 mass NH3 14.007 mass NC2 14.007 mass O 15.999 mass OC 15.999 mass OH1 15.999 mass SH1E 32.060 mass SM 32.060 mass S 32.060 residue ALA group atom N type=NH1 charge=-0.570 end atom HN type=H charge= 0.370 end atom CA type=CH1E charge= 0.200 end atom HA type=HA charge= 0.000 end atom CB type=CH3E charge= 0.000 end atom HB1 type=HA charge= 0.000 end atom HB2 type=HA charge= 0.000 end atom HB3 type=HA charge= 0.000 end atom C type=C charge= 0.500 end atom O type=O charge=-0.500 end bond N HN bond N CA bond CA HA bond CA CB bond CB HB1 bond CB HB2 bond CB HB3 bond CA C bond C O improper HA N C CB !chirality CA improper HB1 HB2 CA HB3 !methyl CB DONO HN N ACCE O C end residue ARG group atom N type=NH1 charge=-0.570 end atom HN type=H charge= 0.370 end atom CA type=CH1E charge= 0.200 end atom HA type=HA charge= 0.000 end atom CB type=CH2E charge= 0.000 end atom HB1 type=HA charge= 0.000 end atom HB2 type=HA charge= 0.000 end atom CG type=CH2E charge= 0.070 end atom HG1 type=HA charge= 0.000 end atom HG2 type=HA charge= 0.000 end atom CD type=CH2E charge= 0.310 end atom HD1 type=HA charge= 0.000 end atom HD2 type=HA charge= 0.000 end atom NE type=NH1 charge=-0.700 end atom HE type=H charge= 0.440 end atom CZ type=C charge= 0.640 end atom NH1 type=NC2 charge=-0.800 end atom HH11 type=HC charge= 0.460 end atom HH12 type=HC charge= 0.460 end atom NH2 type=NC2 charge=-0.800 end atom HH21 type=HC charge= 0.460 end atom HH22 type=HC charge= 0.460 end atom C type=C charge= 0.500 end atom O type=O charge=-0.500 end bond N HN bond N CA bond CA HA bond CA CB bond CB HB1 bond CB HB2 bond CB CG bond CG HG1 bond CG HG2 bond CG CD bond CD HD1 bond CD HD2 bond CD NE bond NE HE bond NE CZ bond CZ NH1 bond NH1 HH11 bond NH1 HH12 bond CZ NH2 bond NH2 HH21 bond NH2 HH22 bond CA C bond C O improper HA N C CB !chirality CA improper NE CD CZ HE improper CZ NE NH1 NH2 improper NH1 CZ HH11 HH12 improper NH2 CZ HH21 HH22 improper NE CZ NH1 HH11 improper NE CZ NH2 HH21 improper CZ NH2 HE NE ! planar HE, CZ improper HB1 HB2 CA CG !stereo CB improper HG1 HG2 CB CD !stereo CG improper HD1 HD2 CG NE !stereo CD dihedral CG CB CA N dihedral CD CG CB CA dihedral NE CD CG CB dihedral CZ NE CD CG DONO HN N DONO HE NE DONO HH11 NH1 DONO HH12 NH1 DONO HH21 NH2 DONO HH22 NH2 ACCE O C end residue ASN group atom N type=NH1 charge=-0.570 end atom HN type=H charge= 0.370 end atom CA type=CH1E charge= 0.200 end atom HA type=HA charge= 0.000 end atom CB type=CH2E charge=-0.000 end atom HB1 type=HA charge= 0.000 end atom HB2 type=HA charge= 0.000 end atom CG type=C charge= 0.500 end atom OD1 type=O charge=-0.500 end atom ND2 type=NH2 charge=-0.850 end atom HD21 type=H charge= 0.425 end atom HD22 type=H charge= 0.425 end atom C type=C charge= 0.500 end atom O type=O charge=-0.500 end bond N HN bond N CA bond CA HA bond CA CB bond CB HB1 bond CB HB2 bond CB CG bond CG OD1 bond CG ND2 bond ND2 HD21 bond ND2 HD22 bond CA C bond C O improper HA N C CB !chirality CA improper CG CB OD1 ND2 improper ND2 CG HD21 HD22 improper CB CG ND2 HD21 improper HB1 HB2 CA CG !stereo CB dihedral CG CB CA N dihedral OD1 CG CB CA DONO HN N DONO HD21 ND2 DONO HD22 ND2 ACCE OD1 CG ACCE O C end residue ASP group atom N type=NH1 charge=-0.570 end atom HN type=H charge= 0.370 end atom CA type=CH1E charge= 0.200 end atom HA type=HA charge= 0.000 end atom CB type=CH2E charge=-0.100 end atom HB1 type=HA charge= 0.000 end atom HB2 type=HA charge= 0.000 end atom CG type=C charge= 0.700 end atom OD1 type=OC charge=-0.800 end atom OD2 type=OC charge=-0.800 end atom C type=C charge= 0.500 end atom O type=O charge=-0.500 end bond N HN bond N CA bond CA HA bond CA CB bond CB HB1 bond CB HB2 bond CB CG bond CG OD1 bond CG OD2 bond CA C bond C O improper HA N C CB !chirality CA improper CG CB OD1 OD2 improper HB1 HB2 CA CG !stereo CB dihedral CG CB CA N dihedral OD1 CG CB CA DONO HN N ACCE OD1 CG ACCE OD2 CG ACCE O C end residue CYS group atom N type=NH1 charge=-0.570 end atom HN type=H charge= 0.370 end atom CA type=CH1E charge= 0.200 end atom HA type=HA charge= 0.000 end atom CB type=CH2E charge= 0.180 end atom HB1 type=HA charge= 0.000 end atom HB2 type=HA charge= 0.000 end atom SG type=SH1E charge=-0.450 end atom HG type=H charge= 0.270 end atom C type=C charge= 0.500 end atom O type=O charge=-0.500 end bond N HN bond N CA bond CA HA bond CA CB bond CB HB1 bond CB HB2 bond CB SG bond SG HG bond CA C bond C O improper HA N C CB !chirality CA improper HB1 HB2 CA SG !stereo CB dihedral SG CB CA N DONO HN N DONO HG SG !!! ACCE SG !REMOVED, ATB ACCE O C end residue GLN group atom N type=NH1 charge=-0.570 end atom HN type=H charge= 0.370 end atom CA type=CH1E charge= 0.200 end atom HA type=HA charge= 0.000 end atom CB type=CH2E charge= 0.000 end atom HB1 type=HA charge= 0.000 end atom HB2 type=HA charge= 0.000 end atom CG type=CH2E charge= 0.000 end atom HG1 type=HA charge= 0.000 end atom HG2 type=HA charge= 0.000 end atom CD type=C charge= 0.500 end atom OE1 type=O charge=-0.500 end atom NE2 type=NH2 charge=-0.850 end atom HE21 type=H charge= 0.425 end atom HE22 type=H charge= 0.425 end atom C type=C charge= 0.500 end atom O type=O charge=-0.500 end bond N HN bond N CA bond CA HA bond CA CB bond CB HB1 bond CB HB2 bond CB CG bond CG HG1 bond CG HG2 bond CG CD bond CD OE1 bond CD NE2 bond NE2 HE21 bond NE2 HE22 bond CA C bond C O improper HA N C CB !chirality CA improper CD CG OE1 NE2 improper NE2 CD HE21 HE22 improper CG CD NE2 HE21 improper HB1 HB2 CA CG !stereo CB improper HG1 HG2 CB CD !stereo CG dihedral CG CB CA N dihedral CD CG CB CA dihedral OE1 CD CG CB DONO HN N DONO HE21 NE2 DONO HE22 NE2 ACCE OE1 CD ACCE O C end residue GLU group atom N type=NH1 charge=-0.570 end atom HN type=H charge= 0.370 end atom CA type=CH1E charge= 0.200 end atom HA type=HA charge= 0.000 end atom CB type=CH2E charge= 0.000 end atom HB1 type=HA charge= 0.000 end atom HB2 type=HA charge= 0.000 end atom CG type=CH2E charge=-0.100 end atom HG1 type=HA charge= 0.000 end atom HG2 type=HA charge= 0.000 end atom CD type=C charge= 0.700 end atom OE1 type=OC charge=-0.800 end atom OE2 type=OC charge=-0.800 end atom C type=C charge= 0.500 end atom O type=O charge=-0.500 end bond N HN bond N CA bond CA HA bond CA CB bond CB HB1 bond CB HB2 bond CB CG bond CG HG1 bond CG HG2 bond CG CD bond CD OE1 bond CD OE2 bond CA C bond C O improper HA N C CB !chirality CA improper CD CG OE1 OE2 improper HB1 HB2 CA CG !stereo CB improper HG1 HG2 CB CD !stereo CG dihedral CG CB CA N dihedral CD CG CB CA dihedral OE1 CD CG CB DONO HN N ACCE OE1 CD ACCE OE2 CD ACCE O C end residue GLY group atom N type=NH1 charge=-0.570 end atom HN type=H charge= 0.370 end atom CA type=CH2G charge= 0.200 end atom HA1 type=HA charge= 0.000 end atom HA2 type=HA charge= 0.000 end atom C type=C charge= 0.500 end atom O type=O charge=-0.500 end bond N HN bond N CA bond CA HA1 bond CA HA2 bond CA C bond C O DONO HN N ACCE O C improper HA1 HA2 N C !stereo CA end residue HISH group atom N type=NH1 charge=-0.570 end atom HN type=H charge= 0.370 end atom CA type=CH1E charge= 0.200 end atom HA type=HA charge= 0.000 end atom CB type=CH2E charge= 0.000 end atom HB1 type=HA charge= 0.000 end atom HB2 type=HA charge= 0.000 end atom CG type=C5 charge= 0.330 end atom ND1 type=NH1 charge=-0.540 end atom HD1 type=H charge= 0.460 end atom CD2 type=CR1H charge= 0.330 end atom HD2 type=HA charge= 0.000 end atom CE1 type=CRHH charge= 0.500 end atom HE1 type=HA charge= 0.000 end atom NE2 type=NH1 charge=-0.540 end atom HE2 TYPE=H charge= 0.460 END !# atom C type=C charge= 0.500 end atom O type=O charge=-0.500 end bond N HN bond N CA bond CA HA bond CA CB bond CB HB1 bond CB HB2 bond CB CG bond CG ND1 bond ND1 HD1 bond ND1 CE1 bond CE1 HE1 bond CG CD2 bond CD2 HD2 bond CD2 NE2 bond NE2 HE2 bond CE1 NE2 bond CA C bond C O improper HA N C CB !chirality CA improper CG CB ND1 CD2 improper ND1 CE1 CG HD1 improper CD2 NE2 CG HD2 improper CE1 ND1 NE2 HE1 improper CG ND1 CE1 NE2 improper ND1 CE1 NE2 CD2 improper CE1 NE2 CD2 CG improper NE2 CD2 CG ND1 improper CD2 CG ND1 CE1 improper HB1 HB2 CA CG !stereo CB dihedral CG CB CA N dihedral ND1 CG CB CA DONO HN N DONO HD1 ND1 DONO HE2 NE2 ACCE O C end residue HIS group atom N type=NH1 charge=-0.570 end atom HN type=H charge= 0.370 end atom CA type=CH1E charge= 0.200 end atom HA type=HA charge= 0.000 end atom CB type=CH2E charge= 0.000 end atom HB1 type=HA charge= 0.000 end atom HB2 type=HA charge= 0.000 end atom CG type=C5 charge= 0.330 end atom ND1 type=NH1 charge=-0.540 end atom HD1 type=H charge= 0.460 end atom CD2 type=CR1H charge= 0.330 end atom HD2 type=HA charge= 0.000 end atom CE1 type=CRHH charge= 0.500 end atom HE1 type=HA charge= 0.000 end atom NE2 type=NH1 charge=-0.540 end atom HE2 TYPE=H charge= 0.460 end atom C type=C charge= 0.500 end atom O type=O charge=-0.500 end bond N HN bond N CA bond CA HA bond CA CB bond CB HB1 bond CB HB2 bond CB CG bond CG ND1 bond ND1 HD1 bond ND1 CE1 bond CE1 HE1 bond CG CD2 bond CD2 HD2 bond CD2 NE2 bond NE2 HE2 bond CE1 NE2 bond CA C bond C O improper HA N C CB !chirality CA improper CG CB ND1 CD2 improper ND1 CE1 CG HD1 improper CD2 NE2 CG HD2 improper CE1 ND1 NE2 HE1 improper CG ND1 CE1 NE2 improper ND1 CE1 NE2 CD2 improper CE1 NE2 CD2 CG improper NE2 CD2 CG ND1 improper CD2 CG ND1 CE1 improper HB1 HB2 CA CG !stereo CB dihedral CG CB CA N dihedral ND1 CG CB CA DONO HN N DONO HD1 ND1 DONO HE2 NE2 ACCE O C end residue ILE group atom N type=NH1 charge=-0.570 end atom HN type=H charge= 0.370 end atom CA type=CH1E charge= 0.200 end atom HA type=HA charge= 0.000 end atom CB type=CH1E charge= 0.000 end atom HB type=HA charge= 0.000 end atom CG1 type=CH2E charge= 0.000 end atom HG11 type=HA charge= 0.000 excl = (HG21 HG22 HG23 HD11 HD12 HD13) end atom HG12 type=HA charge= 0.000 excl = (HG21 HG22 HG23 HD11 HD12 HD13) end atom CG2 type=CH3E charge= 0.000 end atom HG21 type=HA charge= 0.000 excl = (HG11 HG12 HD11 HD12 HD13) end atom HG22 type=HA charge= 0.000 excl = (HG11 HG12 HD11 HD12 HD13) end atom HG23 type=HA charge= 0.000 excl = (HG11 HG12 HD11 HD12 HD13) end atom CD1 type=CH3E charge= 0.000 end atom HD11 type=HA charge= 0.000 excl = (HG21 HG22 HG23 HG11 HG12) end atom HD12 type=HA charge= 0.000 excl = (HG21 HG22 HG23 HG11 HG12) end atom HD13 type=HA charge= 0.000 excl = (HG21 HG22 HG23 HG11 HG12) end atom C type=C charge= 0.500 end atom O type=O charge=-0.500 end bond N HN bond N CA bond CA HA bond CA CB bond CB HB bond CB CG1 bond CG1 HG11 bond CG1 HG12 bond CB CG2 bond CG2 HG21 bond CG2 HG22 bond CG2 HG23 bond CG1 CD1 bond CD1 HD11 bond CD1 HD12 bond CD1 HD13 bond CA C bond C O improper HA N C CB !chirality CA improper HB CA CG2 CG1 !chirality CB improper HG11 HG12 CB CD1 !stereo CG1 improper HG21 HG22 CB HG23 !methyl CG2 improper HD11 HD12 CG1 HD13 !methyl CD1 dihedral CG1 CB CA N dihedral CD1 CG1 CB CA DONO HN N ACCE O C end residue LEU group atom N type=NH1 charge=-0.570 end atom HN type=H charge= 0.370 end atom CA type=CH1E charge= 0.200 end atom HA type=HA charge= 0.000 end atom CB type=CH2E charge= 0.000 end atom HB1 type=HA charge= 0.000 end atom HB2 type=HA charge= 0.000 end atom CG type=CH1E charge= 0.000 end atom HG type=HA charge= 0.000 end atom CD1 type=CH3E charge= 0.000 end atom HD11 type=HA charge= 0.000 excl = (HD21 HD22 HD23 HG) end atom HD12 type=HA charge= 0.000 excl = (HD21 HD22 HD23 HG) end atom HD13 type=HA charge= 0.000 excl = (HD21 HD22 HD23 HG) end atom CD2 type=CH3E charge= 0.000 end atom HD21 type=HA charge= 0.000 excl = (HD11 HD12 HD13 HG) end atom HD22 type=HA charge= 0.000 excl = (HD11 HD12 HD13 HG) end atom HD23 type=HA charge= 0.000 excl = (HD11 HD12 HD13 HG) end atom C type=C charge= 0.500 end atom O type=O charge=-0.500 end bond N HN bond N CA bond CA HA bond CA CB bond CB HB1 bond CB HB2 bond CB CG bond CG HG bond CG CD1 bond CD1 HD11 bond CD1 HD12 bond CD1 HD13 bond CG CD2 bond CD2 HD21 bond CD2 HD22 bond CD2 HD23 bond CA C bond C O improper HA N C CB !chirality CA improper HG CB CD1 CD2 !stereo CG improper HB1 HB2 CA CG !stereo CB improper HD11 HD12 CG HD13 !methyl CD1 improper HD21 HD22 CG HD23 !methyl CD2 dihedral CG CB CA N dihedral CD1 CG CB CA DONO HN N ACCE O C end residue LYS group atom N type=NH1 charge=-0.570 end atom HN type=H charge= 0.370 end atom CA type=CH1E charge= 0.200 end atom HA type=HA charge= 0.000 end atom CB type=CH2E charge= 0.000 end atom HB1 type=HA charge= 0.000 end atom HB2 type=HA charge= 0.000 end atom CG type=CH2E charge= 0.000 end atom HG1 type=HA charge= 0.000 end atom HG2 type=HA charge= 0.000 end atom CD type=CH2E charge= 0.000 end atom HD1 type=HA charge= 0.000 end atom HD2 type=HA charge= 0.000 end atom CE type=CH2E charge= 0.310 end atom HE1 type=HA charge= 0.000 end atom HE2 type=HA charge= 0.000 end atom NZ type=NH3 charge=-0.300 end atom HZ1 type=HC charge= 0.330 end atom HZ2 type=HC charge= 0.330 end atom HZ3 type=HC charge= 0.330 end atom C type=C charge= 0.500 end atom O type=O charge=-0.500 end bond N HN bond N CA bond CA HA bond CA CB bond CB HB1 bond CB HB2 bond CB CG bond CG HG1 bond CG HG2 bond CG CD bond CD HD1 bond CD HD2 bond CD CE bond CE HE1 bond CE HE2 bond CE NZ bond NZ HZ1 bond NZ HZ2 bond NZ HZ3 bond CA C bond C O improper HA N C CB !chirality CA improper HB1 HB2 CA CG !stereo CB improper HG1 HG2 CB CD !stereo CG improper HD1 HD2 CG CE !stereo CD improper HE1 HE2 CD NZ !stereo CE improper HZ1 HZ2 CE HZ3 !methyl NZ dihedral CG CB CA N dihedral CD CG CB CA dihedral CE CD CG CB dihedral NZ CE CD CG DONO HN N DONO HZ1 NZ DONO HZ2 NZ DONO HZ3 NZ ACCE O C end residue MET group atom N type=NH1 charge=-0.570 end atom HN type=H charge= 0.370 end atom CA type=CH1E charge= 0.200 end atom HA type=HA charge= 0.000 end atom CB type=CH2E charge=-0.000 end atom HB1 type=HA charge= 0.000 end atom HB2 type=HA charge= 0.000 end atom CG type=CH2E charge= 0.235 end atom HG1 type=HA charge= 0.000 end atom HG2 type=HA charge= 0.000 end atom SD type=SM charge=-0.470 end atom CE type=CH3E charge= 0.235 end atom HE1 type=HA charge= 0.000 end atom HE2 type=HA charge= 0.000 end atom HE3 type=HA charge= 0.000 end atom C type=C charge= 0.500 end atom O type=O charge=-0.500 end bond N HN bond N CA bond CA HA bond CA CB bond CB HB1 bond CB HB2 bond CB CG bond CG HG1 bond CG HG2 bond CG SD bond SD CE bond CE HE1 bond CE HE2 bond CE HE3 bond CA C bond C O improper HA N C CB !chirality CA improper HB1 HB2 CA CG !stereo CB improper HG1 HG2 CB SD !stereo CG improper HE1 HE2 SD HE3 !methyl CE dihedral CG CB CA N dihedral SD CG CB CA dihedral CE SD CG CB DONO HN N ACCE O C end residue PHE group atom N type=NH1 charge=-0.570 end atom HN type=H charge= 0.370 end atom CA type=CH1E charge= 0.200 end atom HA type=HA charge= 0.000 end atom CB type=CH2E charge= 0.000 end atom HB1 type=HA charge= 0.000 end atom HB2 type=HA charge= 0.000 end atom CG type=CF charge= 0.000 exclude=(CZ) end atom CD1 type=CR1E charge= 0.000 exclude=(CE2) end atom HD1 type=HA charge= 0.000 end atom CD2 type=CR1E charge= 0.000 exclude=(CE1) end atom HD2 type=HA charge= 0.000 end atom CE1 type=CR1E charge= 0.000 exclude=(CD2) end atom HE1 type=HA charge= 0.000 end atom CE2 type=CR1E charge= 0.000 exclude=(CD1) end atom HE2 type=HA charge= 0.000 end atom CZ type=CR1E charge= 0.000 exclude=(CG) end atom HZ type=HA charge= 0.000 end atom C type=C charge= 0.500 end atom O type=O charge=-0.500 end bond N HN bond N CA bond CA HA bond CA CB bond CB HB1 bond CB HB2 bond CB CG bond CG CD1 bond CD1 HD1 bond CG CD2 bond CD2 HD2 bond CD1 CE1 bond CE1 HE1 bond CD2 CE2 bond CE2 HE2 bond CE1 CZ bond CZ HZ bond CE2 CZ bond CA C bond C O improper HA N C CB !chirality CA improper HB1 HB2 CA CG !stereo CB ! Hs and CB around the ring improper HD2 CD2 CE2 CZ improper HE2 CE2 CZ CE1 improper HZ CZ CE1 CD1 improper HE1 CE1 CD1 CG improper HD1 CD1 CG CD2 improper CB CG CD2 CE2 ! around the ring improper CG CD1 CE1 CZ improper CD1 CE1 CZ CE2 improper CE1 CZ CE2 CD2 improper CZ CE2 CD2 CG improper CE2 CD2 CG CD1 improper CD2 CG CD1 CE1 dihedral CG CB CA N dihedral CD1 CG CB CA DONO HN N ACCE O C end residue PRO group atom N type=N charge=-0.570 end atom CA type=CH1E charge= 0.285 end atom HA type=HA charge= 0.000 end atom CB type=CH2E charge= 0.000 end atom HB1 type=HA charge= 0.000 end atom HB2 type=HA charge= 0.000 end atom CG type=CH2P charge= 0.000 end atom HG1 type=HA charge= 0.000 end atom HG2 type=HA charge= 0.000 end atom CD type=CH2P charge= 0.285 end atom HD1 type=HA charge= 0.000 end atom HD2 type=HA charge= 0.000 end atom C type=C charge= 0.500 end atom O type=O charge=-0.500 end bond N CA bond CA HA bond CA CB bond CB HB1 bond CB HB2 bond CB CG bond CG HG1 bond CG HG2 bond CG CD bond CD HD1 bond CD HD2 bond CD N bond CA C bond C O improper HA N C CB !chirality CA improper HB1 HB2 CA CG !stereo CB improper HG1 HG2 CB CD !stereo CG improper HD1 HD2 CG N !stereo CD ACCE O C end residue SER group atom N type=NH1 charge=-0.570 end atom HN type=H charge= 0.370 end atom CA type=CH1E charge= 0.200 end atom HA type=HA charge= 0.000 end atom CB type=CH2E charge= 0.265 end atom HB1 type=HA charge= 0.000 end atom HB2 type=HA charge= 0.000 end atom OG type=OH1 charge=-0.700 end atom HG type=H charge= 0.435 end atom C type=C charge= 0.500 end atom O type=O charge=-0.500 end bond N HN bond N CA bond CA HA bond CA CB bond CB HB1 bond CB HB2 bond CB OG bond OG HG bond O C bond C CA improper HA N C CB !chirality CA improper HB1 HB2 CA OG !stereo CB dihedral OG CB CA N DONO HN N DONO HG OG ACCE OG " " ACCE O C end residue THR group atom N type=NH1 charge=-0.570 end atom HN type=H charge= 0.370 end atom CA type=CH1E charge= 0.200 end atom HA type=HA charge= 0.000 end atom CB type=CH2E charge= 0.265 end atom HB type=HA charge= 0.000 end atom OG1 type=OH1 charge=-0.700 end atom HG1 type=H charge= 0.435 end atom CG2 type=CH3E charge=-0.000 end atom HG21 type=HA charge= 0.000 end atom HG22 type=HA charge= 0.000 end atom HG23 type=HA charge= 0.000 end atom C type=C charge= 0.500 end atom O type=O charge=-0.500 end bond N HN bond N CA bond CA HA bond CA CB bond CB HB bond CB OG1 bond OG1 HG1 bond CB CG2 bond CG2 HG21 bond CG2 HG22 bond CG2 HG23 bond CA C bond C O improper HA N C CB !chirality CA improper HB CA OG1 CG2 !stereo CB improper HG21 HG22 CB HG23 !methyl CG2 dihedral OG1 CB CA N DONO HN N DONO HG1 OG1 ACCE OG1 " " ACCE O C end residue TRP group atom N type=NH1 charge=-0.570 end atom HN type=H charge= 0.370 end atom CA type=CH1E charge= 0.200 end atom HA type=HA charge= 0.000 end atom CB type=CH2E charge= 0.000 end atom HB1 type=HA charge= 0.000 end atom HB2 type=HA charge= 0.000 end atom CG type=C5W charge=-0.055 end atom CD1 type=CR1E charge= 0.130 end atom HD1 type=HA charge= 0.000 end atom CD2 type=CW charge=-0.055 exclude=(CH2) end atom NE1 type=NH1 charge=-0.570 end atom HE1 type=H charge= 0.420 end atom CE2 type=CW charge= 0.130 exclude=(CZ3) end atom CE3 type=CR1E charge= 0.000 exclude=(CZ2) end atom HE3 type=HA charge= 0.000 end atom CZ2 type=CR1W charge= 0.000 exclude=(CE3) end atom HZ2 type=HA charge= 0.000 end atom CZ3 type=CR1E charge= 0.000 exclude=(CE2) end atom HZ3 type=HA charge= 0.000 end atom CH2 type=CR1W charge= 0.000 exclude=(CD2) end atom HH2 type=HA charge= 0.000 end atom C type=C charge= 0.500 end atom O type=O charge=-0.500 end bond N HN bond N CA bond CA HA bond CA CB bond CB HB1 bond CB HB2 bond CB CG bond CG CD1 bond CD1 HD1 bond CG CD2 bond CD1 NE1 bond NE1 HE1 bond NE1 CE2 bond CD2 CE2 bond CD2 CE3 bond CE3 HE3 bond CE2 CZ2 bond CZ2 HZ2 bond CE3 CZ3 bond CZ3 HZ3 bond CZ2 CH2 bond CH2 HH2 bond CZ3 CH2 bond CA C bond C O ! chirality improper HA N C CB !chirality CA improper HB1 HB2 CA CG !stereo CB ! around the 6-ring improper CD2 CE2 CZ2 CH2 improper CE2 CZ2 CH2 CZ3 improper CZ2 CH2 CZ3 CE3 improper CH2 CZ3 CE3 CD2 improper CZ3 CE3 CD2 CE2 improper CE3 CD2 CE2 CZ2 ! link 5-ring to 6-ring improper CD1 NE1 CE2 CZ2 improper CD1 CG CD2 CE3 improper NE1 CE2 CZ2 CH2 improper NE1 CE2 CD2 CE3 improper CG CD2 CE3 CZ3 improper CG CD2 CE2 CZ2 ! 6-ring hydrogens improper HZ2 CZ2 CH2 CZ3 improper HH2 CH2 CZ3 CE3 improper HZ3 CZ3 CH2 CZ2 improper HE3 CE3 CZ3 CH2 ! 5-ring hydrogens and CB improper HE1 NE1 CE2 CD2 improper HD1 CD1 NE1 CE2 improper CB CG CD2 CE2 dihedral CG CB CA N dihedral CD1 CG CB CA DONO HN N DONO HE1 NE1 ACCE O C end residue TYR group atom N type=NH1 charge=-0.570 end atom HN type=H charge= 0.370 end atom CA type=CH1E charge= 0.200 end atom HA type=HA charge= 0.000 end atom CB type=CH2E charge= 0.000 end atom HB1 type=HA charge= 0.000 end atom HB2 type=HA charge= 0.000 end atom CG type=CY charge= 0.000 exclude=(CZ) end atom CD1 type=CR1E charge= 0.000 exclude=(CE2) end atom HD1 type=HA charge= 0.000 end atom CD2 type=CR1E charge= 0.000 exclude=(CE1) end atom HD2 type=HA charge= 0.000 end atom CE1 type=CR1E charge= 0.000 exclude=(CD2) end atom HE1 type=HA charge= 0.000 end atom CE2 type=CR1E charge= 0.000 exclude=(CD1) end atom HE2 type=HA charge= 0.000 end atom CZ type=CY2 charge= 0.265 exclude=(CG) end atom OH type=OH1 charge=-0.700 end atom HH type=H charge= 0.435 end atom C type=C charge= 0.500 end atom O type=O charge=-0.500 end bond N HN bond N CA bond CA HA bond CA CB bond CB HB1 bond CB HB2 bond CB CG bond CG CD1 bond CD1 HD1 bond CG CD2 bond CD2 HD2 bond CD1 CE1 bond CE1 HE1 bond CD2 CE2 bond CE2 HE2 bond CE1 CZ bond CE2 CZ bond CZ OH bond OH HH bond CA C bond C O ! chirality improper HA N C CB !chirality CA improper HB1 HB2 CA CG !stereo CB ! Hs, OH, and CB around the ring improper HD2 CD2 CE2 CZ improper HE2 CE2 CZ CE1 improper OH CZ CE1 CD1 improper HE1 CE1 CD1 CG improper HD1 CD1 CG CD2 improper CB CG CD2 CE2 ! around the ring improper CG CD1 CE1 CZ improper CD1 CE1 CZ CE2 improper CE1 CZ CE2 CD2 improper CZ CE2 CD2 CG improper CE2 CD2 CG CD1 improper CD2 CG CD1 CE1 dihedral CG CB CA N dihedral CD1 CG CB CA DONO HN N DONO HH OH ACCE OH " " ACCE O C end residue VAL group atom N type=NH1 charge=-0.570 end atom HN type=H charge= 0.370 end atom CA type=CH1E charge= 0.200 end atom HA type=HA charge= 0.000 end atom CB type=CH1E charge= 0.000 end atom HB type=HA charge= 0.000 end atom CG1 type=CH3E charge= 0.000 end atom HG11 type=HA charge= 0.000 excl = (HG21 HG22 HG23) end atom HG12 type=HA charge= 0.000 excl = (HG21 HG22 HG23) end atom HG13 type=HA charge= 0.000 excl = (HG21 HG22 HG23) end atom CG2 type=CH3E charge=-0.000 end atom HG21 type=HA charge= 0.000 excl = (HG11 HG12 HG13) end atom HG22 type=HA charge= 0.000 excl = (HG11 HG12 HG13) end atom HG23 type=HA charge= 0.000 excl = (HG11 HG12 HG13) end atom C type=C charge= 0.500 end atom O type=O charge=-0.500 end bond N HN bond N CA bond CA HA bond CA CB bond CB HB bond CB CG1 bond CG1 HG11 bond CG1 HG12 bond CG1 HG13 bond CB CG2 bond CG2 HG21 bond CG2 HG22 bond CG2 HG23 bond CA C bond C O improper HA N C CB !chirality CA improper HB CA CG1 CG2 !stereo CB improper HG11 HG12 CB HG13 !methyl G1 improper HG21 HG22 CB HG23 !methyl G2 dihedral CG1 CB CA N DONO HN N ACCE O C end residue CHEX !! ADDED BY MN group atom N type=NH1 charge=-0.360 end atom HN type=H charge= 0.260 end atom CA type=CH1E charge= 0.000 end atom HA type=HA charge= 0.100 end atom CB type=CH2E charge=-0.200 end atom HB1 type=HA charge= 0.100 end atom HB2 type=HA charge= 0.100 end atom CG type=CH1E charge=-0.200 end atom HG type=HA charge= 0.100 end atom CD1 type=CH2E charge=-0.200 end atom HD11 type=HA charge= 0.100 end atom HD12 type=HA charge= 0.100 end atom CD2 type=CH2E charge=-0.200 end atom HD21 type=HA charge= 0.100 end atom HD22 type=HA charge= 0.100 end atom CE1 type=CH2E charge=-0.200 end atom HE11 type=HA charge= 0.100 end atom HE12 type=HA charge= 0.100 end atom CE2 type=CH2E charge=-0.200 end atom HE21 type=HA charge= 0.100 end atom HE22 type=HA charge= 0.100 end atom CZ type=CH2E charge=-0.200 end atom HZ1 type=HA charge= 0.100 end atom HZ2 type=HA charge= 0.100 end atom C type=C charge= 0.480 end atom O type=O charge=-0.480 end bond N HN bond N CA bond CA HA bond CA CB bond CB HB1 bond CB HB2 bond CB CG bond CG CD1 bond CG CD2 bond CG HG bond CD1 CE1 bond CD1 HD11 bond CD1 HD12 bond CD2 CE2 bond CD2 HD21 bond CD2 HD22 bond CE1 CZ bond CE1 HE11 bond CE1 HE12 bond CE2 CZ bond CE2 HE21 bond CE2 HE22 bond CZ HZ1 bond CZ HZ2 bond CA C bond C O improper HA N C CB !chirality CA improper HB1 HB2 CA CG !stereo CB improper HG CB CD1 CD2 !stereo CG improper HD11 HD12 CG CE1 !stereo CD1 improper HD21 HD22 CG CE2 !stereo CD2 improper HE11 HE12 CE1 CZ !stereo CE1 improper HE11 HE22 CE2 CZ !stereo CE2 improper HZ1 HZ2 CE1 CE2 !stereo CZ dihedral CG CB CA N dihedral CD1 CG CB CA DONO HN N ACCE O C end residue ACE group atom CA type=CH3E charge= 0.000 end atom HA1 type=HA charge= 0.000 end atom HA2 type=HA charge= 0.000 end atom HA3 type=HA charge= 0.000 end atom C type=C charge= 0.500 end atom O type=O charge=-0.500 end bond C CA bond CA HA1 bond CA HA2 bond CA HA3 bond C O improper HA1 HA2 C HA3 !methyl CA ACCE O C end presidue NTER ! patch as "NTER - *" to any except PRO group modify atom +N type=NH3 charge=-0.300 end delete atom +HN end add atom +HT1 type=HC charge= 0.330 end add atom +HT2 type=HC charge= 0.330 end add atom +HT3 type=HC charge= 0.330 end modify atom +CA charge= 0.310 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 improper +HT1 +HT2 +CA +HT3 !methyl N ??? ADD DONOr +HT1 +N ADD DONOr +HT2 +N ADD DONOr +HT3 +N end presidue PROP ! N-terminal for PRO: "PROP - PRO" ! the charges are guessed from making the residue have charge +1 ! and keeping the same charge on N as in NTER (Michael Nilges) modify atom +CD charge= 0.320 end modify atom +CA charge= 0.320 end modify atom +N type=NH3 charge=-0.300 end add atom +HT1 type=HC charge= 0.330 end add atom +HT2 type=HC charge= 0.330 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 improper +HT1 +HT2 +CA +CD !stereo N ADD DONOr +HT1 +N ADD DONOr +HT2 +N end presidue CTER ! C-terminal for all amino acids "* - CTER" ! charge on -C changed from 0.700 to make group -1, Michael Nilges group modify atom -CA charge= 0.100 end modify atom -C charge= 0.700 end delete atom -O end add atom -OT1 type=OC charge=-0.800 end add atom -OT2 type=OC charge=-0.800 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 improper -C -CA -OT2 -OT1 ADD ACCEptor -OT1 -C ADD ACCEptor -OT2 -C end presidue CTN ! C-terminal for all, CONH2 at end "* - CTN" ! charges not consistent with rest, Michael Nilges group modify atom -C charge= 0.48 end modify atom -O charge=-0.48 end add atom -NT type=NH2 charge=-0.52 end add atom -H1 type=H charge= 0.26 end add atom -H2 type=H charge= 0.26 end add bond -C -NT add bond -NT -H1 add bond -NT -H2 add angle -CA -C -NT add angle -O -C -NT add angle -CA -C -O add angle -C -NT -H1 add angle -C -NT -H2 add angle -H1 -NT -H2 add improper -C -CA -NT -O add improper -C -NT -O -H1 add improper -NT -H1 -H2 -C ADD DONOR -H1 -NT ADD DONOR -H2 -NT end presidue PEPT ! PEPTide bond link, for all except the *(-) - (+)PRO link ! "*(-) - PEPT - (+)*: add bond -C +N add angle -CA -C +N add angle -O -C +N add angle -C +N +CA add angle -C +N +HN add improper -O -C +N +CA ! planar -C fixed for DG by JK add improper +HN +N -C -CA ! planar +N add improper -CA -C +N +CA ! planar peptide " end 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 improper -O -C +N +CA ! planar -C add improper +CD +N -C -CA ! planar +N modified, again add improper -CA -C +N +CA ! planar peptide end presidue DISU ! disulfide bridge ...CYS - DISU - CYS... group delete atom 1HG end modify atom 1CB charge= 0.300 end MODIfy ATOM 1SG TYPE=S charge=-0.300 end group delete atom 2HG end modify atom 2CB charge= 0.300 end MODIfy ATOM 2SG TYPE=S charge=-0.300 end add bond 1SG 2SG add angle 1CB 1SG 2SG add angle 1SG 2SG 2CB end presidue DISN ! disulfide bridge ...CYS - DISU - CYS... ! w/o the actual bond group delete atom 1HG end modify atom 1CB charge= 0.300 end MODIfy ATOM 1SG TYPE=S charge=-0.300 end group delete atom 2HG end modify atom 2CB charge= 0.300 end MODIfy ATOM 2SG TYPE=S charge=-0.300 end end presidue LTOD ! change from L to D amino acid delete improper HA N C CB add improper HA C N CB end presidue CISP ! change from trans to cis peptide bond delete improper -CA -C +N +CA add improper -C -CA +N +CA delete improper -O -C +N +CA add improper -C -O +N +CA delete improper +HN +N -C -CA add improper +N +HN -C -CA end presidue CIPP ! change from trans to cis peptide bond delete improper -CA -C +N +CA add improper -C -CA +N +CA delete improper -O -C +N +CA add improper -C -O +N +CA ! delete improper +CA +N -C +CD ! add improper +CA +N +CD -C delete improper +CD +N -C -CA add improper +N +CD -C -CA end !-------------------------------------------------------------------------- PRESidue HISE ! Patch to change doubly protonated HIS to singly ! protonated histidine (HE2) ! has to be patched as REFErence=NIL= atom CD1 type=CR1E charge= 0.130 end DELETE DONOR ND1 HD1 MODIFY ATOM CB TYPE=CH2E CHARge= 0.000 END MODIFY ATOM CG TYPE=C5 CHARge= 0.130 END !# MODIFY ATOM ND1 TYPE=NR CHARge=-0.570 END !# MODIFY ATOM CE1 TYPE=CRH CHARge= 0.410 END !# MODIFY ATOM CD2 TYPE=CR1E CHARge= 0.100 END MODIFY ATOM NE2 TYPE=NH1 CHARge=-0.570 END !# MODIFY ATOM HE2 TYPE=H CHARge= 0.420 END !# DELETE ATOM HD1 END ADD ACCEPTOR ND1 " " END {HISE} !-------------------------------------------------------------------------- PRES HISD ! Patch to change doubly protonated HIS to singly ! protonated histidine (HD1) ! has to be patched as REFErence=NIL= DELETE DONOR HE2 NE2 MODIFY ATOM CB TYPE=CH2E CHARge= 0.000 END MODIFY ATOM CG TYPE=C5 CHARge= 0.130 END !# MODIFY ATOM ND1 TYPE=NH1 CHARge=-0.570 END !# MODIFY ATOM HD1 TYPE=H CHARge= 0.420 END !# MODIFY ATOM CD2 TYPE=CR1E CHARge= 0.100 END !# MODIFY ATOM NE2 TYPE=NR CHARge=-0.490 END !# MODIFY ATOM CE1 TYPE=CRH CHARge= 0.410 END !# DELETE ATOM HE2 END ADD ACCEPTOR NE2 " " END {HISD} set echo=true end