! ! xplor-nih protein topology file, version 1.0 ! ! This file is intended to work with the parameter file protein-1.0.par ! ! This is a re-named copy of the file topallhdg_new.pro ! ! We've created this new filename in order to eliminate confusion ! between the various parameter/topology combinations that ship ! with xplor-nih. It has version numbers, and will be updated ! along with the rest of the xplor-nih package. ! ! Its backbone bond lengths and angles are designed to agree with ! the Engh & Huber parameter set (reference below), which is used by ! PROCHECK, among other structure-validation programs. ! ! If you find errors, PLEASE let us know. ! remark file protein-1.0.top remark geometric energy function topology for distance geometry and remark simulated annealing. remark remark history: remark remark XPLOR topology file TOPALLHSA.PRO, all hydrogens, remark for simulated annealing, to be used with PARALLHSA.PRO remark based on TOPALLH6.PRO. remark internal coordinates from TOPH19.PRO. remark doubly protonated histidine. ! all dihedrals defining planarity have been converted to impropers, ! the only dihedrals left are around rotatable bonds. ! some additional impropers were included in the rings to define planarity ! better. patches are included to define chirality at stereospecifically ! assigned prochiral centres and convert from trans to cis peptide bond. ! modifications by M. Nilges and P. Kraulis. ! added stereospecific impropers for all pro-chiral centers (ATB) ! remark corrected proline angles to Engh & Huber, Acta Cryst., A47, 392 (1991) values. remark Needed to define a new atom type, CP, which is equivalent to their remark CH2P atom type. JJK 9/22/95 ! 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 CT 12.011 mass CX 12.011 mass CW 12.011 mass CN 12.011 mass CA 12.011 mass CB 12.011 mass CC 12.011 mass CV 12.011 mass CR 12.011 mass CP 12.011 mass N 14.007 mass NA 14.007 mass NB 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 OH 15.999 mass S 32.060 residue ALA group atom N type=NH1 charge=-0.36 end atom HN type=H charge= 0.26 end group atom CA type=CT charge= 0.00 end atom HA type=HA charge= 0.10 end group atom CB type=CT charge=-0.30 end atom HB1 type=HA charge= 0.10 end atom HB2 type=HA charge= 0.10 end atom HB3 type=HA charge= 0.10 end group atom C type=C charge= 0.48 end atom O type=O charge=-0.48 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 !stereo CA improper HB1 HB2 CA HB3 !stereo CB end residue ARG group atom N type=NH1 charge=-0.36 end atom HN type=H charge= 0.26 end group atom CA type=CT charge= 0.00 end atom HA type=HA charge= 0.10 end group atom CB type=CT charge=-0.20 end atom HB1 type=HA charge= 0.10 end atom HB2 type=HA charge= 0.10 end group atom CG type=CT charge=-0.20 end atom HG1 type=HA charge= 0.10 end atom HG2 type=HA charge= 0.10 end group atom CD type=CT charge=-0.10 end atom HD1 type=HA charge= 0.15 end atom HD2 type=HA charge= 0.15 end group atom NE type=NH1 charge=-0.60 end atom HE type=H charge= 0.40 end group atom CZ type=C charge= 0.60 end group atom NH1 type=NC2 charge=-0.60 end atom HH11 type=HC charge= 0.40 end atom HH12 type=HC charge= 0.40 end group atom NH2 type=NC2 charge=-0.60 end atom HH21 type=HC charge= 0.40 end atom HH22 type=HC charge= 0.40 end group atom C type=C charge= 0.48 end atom O type=O charge=-0.48 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 !stereo 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 NH1 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 end residue ASN group atom N type=NH1 charge=-0.36 end atom HN type=H charge= 0.26 end group atom CA type=CT charge= 0.00 end atom HA type=HA charge= 0.10 end group atom CB type=CT charge=-0.20 end atom HB1 type=HA charge= 0.10 end atom HB2 type=HA charge= 0.10 end group atom CG type=C charge= 0.48 end atom OD1 type=O charge=-0.48 end group atom ND2 type=NH2 charge=-0.52 end atom HD21 type=H charge= 0.26 end atom HD22 type=H charge= 0.26 end group atom C type=C charge= 0.48 end atom O type=O charge=-0.48 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 !stereo 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 end residue ASP group atom N type=NH1 charge=-0.36 end atom HN type=H charge= 0.26 end group atom CA type=CT charge= 0.00 end atom HA type=HA charge= 0.10 end group atom CB type=CT charge=-0.45 end atom HB1 type=HA charge= 0.10 end atom HB2 type=HA charge= 0.10 end group atom CG type=C charge= 0.49 end atom OD1 type=OC charge=-0.62 end atom OD2 type=OC charge=-0.62 end group atom C type=C charge= 0.48 end atom O type=O charge=-0.48 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 !stereo CA improper CG CB OD1 OD2 improper HB1 HB2 CA CG !stereo CB dihedral CG CB CA N dihedral OD1 CG CB CA end residue CYS group atom N type=NH1 charge=-0.36 end atom HN type=H charge= 0.26 end group atom CA type=CT charge= 0.00 end atom HA type=HA charge= 0.10 end group atom CB type=CT charge=-0.20 end atom HB1 type=HA charge= 0.10 end atom HB2 type=HA charge= 0.10 end group atom SG type=S charge=-0.05 end atom HG type=H charge= 0.05 end group atom C type=C charge= 0.48 end atom O type=O charge=-0.48 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 !stereo CA improper HB1 HB2 CA SG !stereo CB dihedral SG CB CA N end residue GLN group atom N type=NH1 charge=-0.36 end atom HN type=H charge= 0.26 end group atom CA type=CT charge= 0.00 end atom HA type=HA charge= 0.10 end group atom CB type=CT charge=-0.20 end atom HB1 type=HA charge= 0.10 end atom HB2 type=HA charge= 0.10 end group atom CG type=CT charge=-0.20 end atom HG1 type=HA charge= 0.10 end atom HG2 type=HA charge= 0.10 end group atom CD type=C charge= 0.48 end atom OE1 type=O charge=-0.48 end group atom NE2 type=NH2 charge=-0.52 end atom HE21 type=H charge= 0.26 end atom HE22 type=H charge= 0.26 end group atom C type=C charge= 0.48 end atom O type=O charge=-0.48 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 !stereo 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 end residue GLU group atom N type=NH1 charge=-0.36 end atom HN type=H charge= 0.26 end group atom CA type=CT charge= 0.00 end atom HA type=HA charge= 0.10 end group atom CB type=CT charge=-0.20 end atom HB1 type=HA charge= 0.10 end atom HB2 type=HA charge= 0.10 end group atom CG type=CT charge=-0.45 end atom HG1 type=HA charge= 0.10 end atom HG2 type=HA charge= 0.10 end group atom CD type=C charge= 0.49 end group atom OE1 type=OC charge=-0.62 end group atom OE2 type=OC charge=-0.62 end group atom C type=C charge= 0.48 end atom O type=O charge=-0.48 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 !stereo 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 end residue GLY group atom N type=NH1 charge=-0.36 end atom HN type=H charge= 0.26 end group atom CA type=CT charge=-0.10 end atom HA1 type=HA charge= 0.10 end atom HA2 type=HA charge= 0.10 end group atom C type=C charge= 0.48 end atom O type=O charge=-0.48 end bond N HN bond N CA bond CA HA1 bond CA HA2 bond CA C bond C O improper HA1 HA2 N C !stereo CA end residue HIS group atom N type=NH1 charge=-0.36 end atom HN type=H charge= 0.26 end group atom CA type=CT charge= 0.00 end atom HA type=HA charge= 0.10 end group atom CB type=CT charge=-0.20 end atom HB1 type=HA charge= 0.10 end atom HB2 type=HA charge= 0.10 end group atom CG type=CC charge= 0.05 end group atom ND1 type=NA charge=-0.40 end atom HD1 type=H charge= 0.40 end group atom CD2 type=CV charge=-0.14 end atom HD2 type=HA charge= 0.14 end group atom CE1 type=CR charge=-0.14 end atom HE1 type=HA charge= 0.14 end group atom NE2 type=NB charge=-0.05 end ATOM HE2 TYPE=H CHARge= 0.35 END !# group atom C type=C charge= 0.48 end atom O type=O charge=-0.48 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 CE1 NE2 bonds NE2 HE2 bond CA C bond C O improper HA N C CB !stereo 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 IMPRoper NE2 CD2 CE1 HE2 !planar NE2 dihedral CG CB CA N dihedral ND1 CG CB CA end residue ILE group atom N type=NH1 charge=-0.36 end atom HN type=H charge= 0.26 end group atom CA type=CT charge= 0.00 end atom HA type=HA charge= 0.10 end group atom CB type=CT charge=-0.10 end atom HB type=HA charge= 0.10 end group atom CG1 type=CT charge=-0.20 end atom HG11 type=HA charge= 0.10 excl = (HG21 HG22 HG23 HD11 HD12 HD13) end atom HG12 type=HA charge= 0.10 excl = (HG21 HG22 HG23 HD11 HD12 HD13) end group atom CG2 type=CT charge=-0.30 end atom HG21 type=HA charge= 0.10 excl = (HG11 HG12 HD11 HD12 HD13) end atom HG22 type=HA charge= 0.10 excl = (HG11 HG12 HD11 HD12 HD13) end atom HG23 type=HA charge= 0.10 excl = (HG11 HG12 HD11 HD12 HD13) end group atom CD1 type=CT charge=-0.30 end atom HD11 type=HA charge= 0.10 excl = (HG21 HG22 HG23 HG11 HG12) end atom HD12 type=HA charge= 0.10 excl = (HG21 HG22 HG23 HG11 HG12) end atom HD13 type=HA charge= 0.10 excl = (HG21 HG22 HG23 HG11 HG12) end group atom C type=C charge= 0.48 end atom O type=O charge=-0.48 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 !stereo CA improper HB CA CG2 CG1 !stereo CB improper HG11 HG12 CB CD1 !stereo CG1 improper HG21 HG22 CB HG23 !stereo CG2 improper HD11 HD12 CG1 HD13 !stereo CD1 dihedral CG1 CB CA N dihedral CD1 CG1 CB CA end residue LEU group atom N type=NH1 charge=-0.36 end atom HN type=H charge= 0.26 end group atom CA type=CT charge= 0.00 end atom HA type=HA charge= 0.10 end group atom CB type=CT charge=-0.20 end atom HB1 type=HA charge= 0.10 end atom HB2 type=HA charge= 0.10 end group atom CG type=CT charge=-0.10 end atom HG type=HA charge= 0.10 end group atom CD1 type=CT charge=-0.30 end atom HD11 type=HA charge= 0.10 excl = (HD21 HD22 HD23 HG) end atom HD12 type=HA charge= 0.10 excl = (HD21 HD22 HD23 HG) end atom HD13 type=HA charge= 0.10 excl = (HD21 HD22 HD23 HG) end group atom CD2 type=CT charge=-0.30 end atom HD21 type=HA charge= 0.10 excl = (HD11 HD12 HD13 HG) end atom HD22 type=HA charge= 0.10 excl = (HD11 HD12 HD13 HG) end atom HD23 type=HA charge= 0.10 excl = (HD11 HD12 HD13 HG) end group atom C type=C charge= 0.48 end atom O type=O charge=-0.48 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 improper HG CB CD1 CD2 !stereo CG improper HB1 HB2 CA CG !stereo CB improper HD11 HD12 CG HD13 !stereo CD1 improper HD21 HD22 CG HD23 !stereo CD2 dihedral CG CB CA N dihedral CD1 CG CB CA end residue LYS group atom N type=NH1 charge=-0.360 end atom HN type=H charge= 0.260 end group atom CA type=CT charge= 0.000 end atom HA type=HA charge= 0.100 end group atom CB type=CT charge=-0.200 end atom HB1 type=HA charge= 0.100 end atom HB2 type=HA charge= 0.100 end group atom CG type=CT charge=-0.200 end atom HG1 type=HA charge= 0.100 end atom HG2 type=HA charge= 0.100 end group atom CD type=CT charge=-0.200 end atom HD1 type=HA charge= 0.100 end atom HD2 type=HA charge= 0.100 end group atom CE type=CT charge= 0.305 end atom HE1 type=HA charge= 0.100 end atom HE2 type=HA charge= 0.100 end group atom NZ type=NH3 charge=-0.810 end atom HZ1 type=HC charge= 0.435 end atom HZ2 type=HC charge= 0.435 end atom HZ3 type=HC charge= 0.435 end group 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 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 !stereo 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 !stereo NZ dihedral CG CB CA N dihedral CD CG CB CA dihedral CE CD CG CB dihedral NZ CE CD CG end residue MET group atom N type=NH1 charge=-0.360 end atom HN type=H charge= 0.260 end group atom CA type=CT charge= 0.000 end atom HA type=HA charge= 0.100 end group atom CB type=CT charge=-0.200 end atom HB1 type=HA charge= 0.100 end atom HB2 type=HA charge= 0.100 end group atom CG type=CT charge=-0.115 end atom HG1 type=HA charge= 0.100 end atom HG2 type=HA charge= 0.100 end group atom SD type=S charge=-0.170 end group atom CE type=CT charge=-0.215 end atom HE1 type=HA charge= 0.100 end atom HE2 type=HA charge= 0.100 end atom HE3 type=HA charge= 0.100 end group 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 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 !stereo CA improper HB1 HB2 CA CG !stereo CB improper HG1 HG2 CB SD !stereo CG improper HE1 HE2 SD HE3 !stereo methyl dihedral CG CB CA N dihedral SD CG CB CA dihedral CE SD CG CB end residue PHE group atom N type=NH1 charge=-0.36 end atom HN type=H charge= 0.26 end group atom CA type=CT charge= 0.00 end atom HA type=HA charge= 0.10 end group atom CB type=CT charge=-0.16 end atom HB1 type=HA charge= 0.10 end atom HB2 type=HA charge= 0.10 end group atom CG type=CA charge= 0.03 exclude=(CZ) end group atom CD1 type=CA charge=-0.16 exclude=(CE2) end atom HD1 type=HA charge= 0.14 end group atom CD2 type=CA charge=-0.16 exclude=(CE1) end atom HD2 type=HA charge= 0.14 end group atom CE1 type=CA charge=-0.15 exclude=(CD2) end atom HE1 type=HA charge= 0.14 end group atom CE2 type=CA charge=-0.15 exclude=(CD1) end atom HE2 type=HA charge= 0.14 end group atom CZ type=CA charge=-0.15 exclude=(CG) end atom HZ type=HA charge= 0.14 end group atom C type=C charge= 0.48 end atom O type=O charge=-0.48 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 !stereo 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 end residue PRO group atom N type=N charge=-0.36 end group atom CA type=CT charge= 0.00 end atom HA type=HA charge= 0.10 end group atom CB type=CT charge=-0.20 end atom HB1 type=HA charge= 0.10 end atom HB2 type=HA charge= 0.10 end group atom CG type=CP charge=-0.20 end atom HG1 type=HA charge= 0.10 end atom HG2 type=HA charge= 0.10 end group atom CD type=CP charge= 0.06 end atom HD2 type=HA charge= 0.10 end ! the order of the two h's atom HD1 type=HA charge= 0.10 end ! is inverted for the sake of group atom C type=C charge= 0.48 end ! hbuild atom O type=O charge=-0.48 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 !stereo CA improper HB1 HB2 CA CG !stereo CB improper HG1 HG2 CB CD !stereo CG improper HD1 HD2 CG N !stereo CD end residue SER group atom N type=NH1 charge=-0.36 end atom HN type=H charge= 0.26 end group atom CA type=CT charge= 0.00 end atom HA type=HA charge= 0.10 end group atom CB type=CT charge= 0.08 end atom HB1 type=HA charge= 0.10 end atom HB2 type=HA charge= 0.10 end group atom OG type=OH charge=-0.68 end atom HG type=H charge= 0.40 end group atom C type=C charge= 0.48 end atom O type=O charge=-0.48 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 !stereo CA improper HB1 HB2 CA OG !stereo CB dihedral OG CB CA N end residue THR group atom N type=NH1 charge=-0.36 end atom HN type=H charge= 0.26 end group atom CA type=CT charge= 0.00 end atom HA type=HA charge= 0.10 end group atom CB type=CT charge= 0.18 end atom HB type=HA charge= 0.10 end group atom OG1 type=OH charge=-0.68 end atom HG1 type=H charge= 0.40 end group atom CG2 type=CT charge=-0.30 end atom HG21 type=HA charge= 0.10 end atom HG22 type=HA charge= 0.10 end atom HG23 type=HA charge= 0.10 end group atom C type=C charge= 0.48 end atom O type=O charge=-0.48 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 !stereo CA improper HB CA OG1 CG2 !stereo CB improper HG21 HG22 CB HG23 !stereo methyl dihedral OG1 CB CA N end residue TRP group atom N type=NH1 charge=-0.36 end atom HN type=H charge= 0.26 end group atom CA type=CT charge= 0.00 end atom HA type=HA charge= 0.10 end group atom CB type=CT charge=-0.20 end atom HB1 type=HA charge= 0.10 end atom HB2 type=HA charge= 0.10 end group atom CG type=CX charge=-0.04 end group atom CD1 type=CW charge=-0.01 end atom HD1 type=HA charge= 0.14 end group atom CD2 type=CB charge=-0.05 exclude=(CH2) end group atom NE1 type=NA charge=-0.49 end atom HE1 type=H charge= 0.40 end group atom CE2 type=CN charge= 0.13 exclude=(CZ3) end group atom CE3 type=CA charge=-0.16 exclude=(CZ2) end atom HE3 type=HA charge= 0.14 end group atom CZ2 type=CA charge=-0.15 exclude=(CE3) end atom HZ2 type=HA charge= 0.14 end group atom CZ3 type=CA charge=-0.15 exclude=(CE2) end atom HZ3 type=HA charge= 0.14 end group atom CH2 type=CA charge=-0.18 exclude=(CD2) end atom HH2 type=HA charge= 0.14 end group atom C type=C charge= 0.48 end atom O type=O charge=-0.48 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 !stereo 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 end residue TYR group atom N type=NH1 charge=-0.36 end atom HN type=H charge= 0.26 end group atom CA type=CT charge= 0.00 end atom HA type=HA charge= 0.10 end group atom CB type=CT charge=-0.20 end atom HB1 type=HA charge= 0.10 end atom HB2 type=HA charge= 0.10 end group atom CG type=CA charge= 0.00 exclude=(CZ) end group atom CD1 type=CA charge=-0.14 exclude=(CE2) end atom HD1 type=HA charge= 0.14 end group atom CD2 type=CA charge=-0.14 exclude=(CE1) end atom HD2 type=HA charge= 0.14 end group atom CE1 type=CA charge=-0.14 exclude=(CD2) end atom HE1 type=HA charge= 0.14 end group atom CE2 type=CA charge=-0.14 exclude=(CD1) end atom HE2 type=HA charge= 0.14 end group atom CZ type=C charge= 0.20 exclude=(CG) end group atom OH type=OH charge=-0.60 end atom HH type=H charge= 0.40 end group atom C type=C charge= 0.48 end atom O type=O charge=-0.48 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 !stereo 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 end residue VAL group atom N type=NH1 charge=-0.36 end atom HN type=H charge= 0.26 end group atom CA type=CT charge= 0.00 end atom HA type=HA charge= 0.10 end group atom CB type=CT charge=-0.10 end atom HB type=HA charge= 0.10 end group atom CG1 type=CT charge=-0.30 end atom HG11 type=HA charge= 0.10 excl = (HG21 HG22 HG23) end atom HG12 type=HA charge= 0.10 excl = (HG21 HG22 HG23) end atom HG13 type=HA charge= 0.10 excl = (HG21 HG22 HG23) end group atom CG2 type=CT charge=-0.30 end atom HG21 type=HA charge= 0.10 excl = (HG11 HG12 HG13) end atom HG22 type=HA charge= 0.10 excl = (HG11 HG12 HG13) end atom HG23 type=HA charge= 0.10 excl = (HG11 HG12 HG13) end group atom C type=C charge= 0.48 end atom O type=O charge=-0.48 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 !stereo CA improper HB CA CG1 CG2 !stereo CB improper HG11 HG12 CB HG13 !stereo G1 improper HG21 HG22 CB HG23 !stereo G2 dihedral CG1 CB CA N end residue CHEX !! ADDED BY MN group atom N type=NH1 charge=-0.360 end atom HN type=H charge= 0.260 end group atom CA type=CT charge= 0.000 end atom HA type=HA charge= 0.100 end group atom CB type=CT charge=-0.200 end atom HB1 type=HA charge= 0.100 end atom HB2 type=HA charge= 0.100 end group atom CG type=CT charge=-0.200 end atom HG type=HA charge= 0.100 end group atom CD1 type=CT charge=-0.200 end atom HD11 type=HA charge= 0.100 end atom HD12 type=HA charge= 0.100 end group atom CD2 type=CT charge=-0.200 end atom HD21 type=HA charge= 0.100 end atom HD22 type=HA charge= 0.100 end group atom CE1 type=CT charge=-0.200 end atom HE11 type=HA charge= 0.100 end atom HE12 type=HA charge= 0.100 end group atom CE2 type=CT charge=-0.200 end atom HE21 type=HA charge= 0.100 end atom HE22 type=HA charge= 0.100 end group atom CZ type=CT charge=-0.200 end atom HZ1 type=HA charge= 0.100 end atom HZ2 type=HA charge= 0.100 end group 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 !stereo 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 end residue ACE group atom CA type=CT charge=-0.30 end atom HA1 type=HA charge= 0.10 end atom HA2 type=HA charge= 0.10 end atom HA3 type=HA charge= 0.10 end group atom C type=C charge= 0.48 end atom O type=O charge=-0.48 end bond C CA bond CA HA1 bond CA HA2 bond CA HA3 bond C O improper HA1 HA2 C HA3 !stereo methyl end presidue NTER ! patch as "NTER - *" to any except PRO modify atom +CA charge= 0.22 end group modify atom +N type=NH3 charge=-0.10 end delete atom +HN end add atom +HT1 type=HC charge= 0.26 end add atom +HT2 type=HC charge= 0.26 end add atom +HT3 type=HC charge= 0.26 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 !stereo N ??? end presidue PROP ! N-terminal for PRO: "PROP - PRO" modify atom +CD charge= 0.10 end modify atom +CA charge= 0.10 end modify atom +N type=NH3 charge=-0.02 end add atom +HT1 type=HC charge= 0.26 end add atom +HT2 type=HC charge= 0.26 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 end presidue CTER ! C-terminal for all amino acids "* - CTER" group modify atom -C charge= 0.14 end delete atom -O end add atom -OT1 type=OC charge=-0.57 end add atom -OT2 type=OC charge=-0.57 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 end presidue CTN ! C-terminal for all, CONH2 at end "* - CTN" 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 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 +CA +N -C +CD ! planar +N modified 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= 0.20 end modify atom 1SG charge=-0.20 end group delete atom 2HG end modify atom 2CB charge= 0.20 end modify atom 2SG charge=-0.20 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= 0.20 end modify atom 1SG charge=-0.20 end group delete atom 2HG end modify atom 2CB charge= 0.20 end modify atom 2SG charge=-0.20 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 ! works for all except the *(-) - (+)PRO link ! use the PATCh statement: ! PATCh REFErence=-=( ) ! REFErence=+=( ) 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 ! special patch for the *(-) - (+)PRO link ! use the PATCh statement: ! PATCh REFErence=-=( ) ! REFErence=+=( ) 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 end ! patch to turn serine into phosphoserine ! this should probably be turned into a distinct residue ! CDS 2005/7/6 ! presidue SP group modify atom 1cb charge=0.0 end modify atom 1og charge=0.0 end delete atom 1hg charge=0.0 end group modify atom 2P charge=0.0 end modify atom 2O1P charge=0.0 end modify atom 2O2P charge=0.0 end modify atom 2O3P charge=0.0 end add bond 1og 2P add angle 1cb 1og 2p add angle 1og 2P 2O1P add angle 1og 2P 2O2P add angle 1og 2P 2O3P end ! patch to turn cysteine into phosphocysteine ! this should probably be turned into a distinct residue ! CDS 2005/7/6 ! presidue CP group modify atom 1cb charge=0.0 end modify atom 1sg charge=0.0 end delete atom 1hg charge=0.0 end group modify atom 2P charge=0.0 end modify atom 2O1P charge=0.0 end modify atom 2O2P charge=0.0 end modify atom 2O3P charge=0.0 end add bond 1sg 2P add angle 1cb 1sg 2p add angle 1sg 2P 2O1P add angle 1sg 2P 2O2P add angle 1sg 2P 2O3P end ! patch to create phosphotyrosine ! ! presidue YP group modify atom 1cz charge=0.0 end modify atom 1oh charge=0.0 end delete atom 1hh charge=0.0 end group modify atom 2P charge=0.0 end modify atom 2O1P charge=0.0 end modify atom 2O2P charge=0.0 end modify atom 2O3P charge=0.0 end add bond 1oh 2P add angle 1cz 1oh 2p add angle 1oh 2P 2O1P add angle 1oh 2P 2O2P add angle 1oh 2P 2O3P end set message=$prev_messages echo=$prev_echo end