log started: Tue May 2 15:27:45 2017 Log file: ./leap.log >> # >> # ----- leaprc for loading the general Amber Force field. >> # This file is mostly for use with Antechamber >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "h1" "H" "sp3" } >> { "h2" "H" "sp3" } >> { "h3" "H" "sp3" } >> { "h4" "H" "sp3" } >> { "h5" "H" "sp3" } >> { "ha" "H" "sp3" } >> { "hc" "H" "sp3" } >> { "hn" "H" "sp3" } >> { "ho" "H" "sp3" } >> { "hp" "H" "sp3" } >> { "hs" "H" "sp3" } >> { "hw" "H" "sp3" } >> { "hx" "H" "sp3" } >> { "o" "O" "sp2" } >> { "o2" "O" "sp2" } >> { "oh" "O" "sp3" } >> { "os" "O" "sp3" } >> { "ow" "O" "sp3" } >> { "c" "C" "sp2" } >> { "c1" "C" "sp2" } >> { "c2" "C" "sp2" } >> { "c3" "C" "sp3" } >> { "ca" "C" "sp2" } >> { "cc" "C" "sp2" } >> { "cd" "C" "sp2" } >> { "ce" "C" "sp2" } >> { "cf" "C" "sp2" } >> { "cg" "C" "sp2" } >> { "ch" "C" "sp2" } >> { "cp" "C" "sp2" } >> { "cq" "C" "sp2" } >> { "cu" "C" "sp2" } >> { "cv" "C" "sp2" } >> { "cx" "C" "sp2" } >> { "cy" "C" "sp2" } >> { "n" "N" "sp2" } >> { "n1" "N" "sp2" } >> { "n2" "N" "sp2" } >> { "n3" "N" "sp3" } >> { "n4" "N" "sp3" } >> { "na" "N" "sp2" } >> { "nb" "N" "sp2" } >> { "nc" "N" "sp2" } >> { "nd" "N" "sp2" } >> { "ne" "N" "sp2" } >> { "nf" "N" "sp2" } >> { "nh" "N" "sp2" } >> { "no" "N" "sp2" } >> { "s" "S" "sp2" } >> { "s2" "S" "sp2" } >> { "s3" "S" "sp3" } >> { "s4" "S" "sp3" } >> { "s6" "S" "sp3" } >> { "sh" "S" "sp3" } >> { "ss" "S" "sp3" } >> { "sx" "S" "sp3" } >> { "sy" "S" "sp3" } >> { "p2" "P" "sp2" } >> { "p3" "P" "sp3" } >> { "p4" "P" "sp3" } >> { "p5" "P" "sp3" } >> { "pb" "P" "sp3" } >> { "pd" "P" "sp3" } >> { "px" "P" "sp3" } >> { "py" "P" "sp3" } >> { "f" "F" "sp3" } >> { "cl" "Cl" "sp3" } >> { "br" "Br" "sp3" } >> { "i" "I" "sp3" } >> } >> # >> # Load the general force field parameter set. >> # >> gaff = loadamberparams gaff.dat Loading parameters: /opt/AMBER/amber12/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic molecules (Version 1.4, March 2010) add. info. at the end (UNKNOWN ATOM TYPE: cz) > > loadamberparams ligand_1.frcmod Loading parameters: ./ligand_1.frcmod Reading force field modification type file (frcmod) Reading title: remark goes here > loadoff pgn.lib Loading library: ./pgn.lib Loading: PGN > loadamberparams frcmod.zinc Loading parameters: ./frcmod.zinc Reading force field modification type file (frcmod) Reading title: Amber Force Field Parameters for the Tetrahedron-Shaped Zinc Divalent Cation (UNKNOWN ATOM TYPE: DZ) (UNKNOWN ATOM TYPE: Zn) > loadoff znb.lib Loading library: ./znb.lib Loading: ZNB > com=loadpdb prot_dock_noh_no_conf.pdb Loading PDB file: ./prot_dock_noh_no_conf.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue SER, term: Terminal/beginning, seq. number: 0 to: NSER. (Residue 1: LEU, Nonterminal, was not found in name map.) (Residue 2: PRO, Nonterminal, was not found in name map.) (Residue 3: LYS, Nonterminal, was not found in name map.) (Residue 4: TYR, Nonterminal, was not found in name map.) (Residue 5: LYS, Nonterminal, was not found in name map.) (Residue 6: PRO, Nonterminal, was not found in name map.) (Residue 7: GLN, Nonterminal, was not found in name map.) (Residue 8: VAL, Nonterminal, was not found in name map.) (Residue 9: ASN, Nonterminal, was not found in name map.) (Residue 10: SER, Nonterminal, was not found in name map.) (Residue 11: SER, Nonterminal, was not found in name map.) (Residue 12: ILE, Nonterminal, was not found in name map.) (Residue 13: ASN, Nonterminal, was not found in name map.) (Residue 14: ASP, Nonterminal, was not found in name map.) (Residue 15: TYR, Nonterminal, was not found in name map.) (Residue 16: ILE, Nonterminal, was not found in name map.) (Residue 17: CYS, Nonterminal, was not found in name map.) (Residue 18: LYS, Nonterminal, was not found in name map.) (Residue 19: ASN, Nonterminal, was not found in name map.) (Residue 20: ASN, Nonterminal, was not found in name map.) (Residue 21: LEU, Nonterminal, was not found in name map.) (Residue 22: LYS, Nonterminal, was not found in name map.) (Residue 23: ALA, Nonterminal, was not found in name map.) (Residue 24: PRO, Nonterminal, was not found in name map.) (Residue 25: LYS, Nonterminal, was not found in name map.) (Residue 26: ILE, Nonterminal, was not found in name map.) (Residue 27: GLU, Nonterminal, was not found in name map.) (Residue 28: GLU, Nonterminal, was not found in name map.) (Residue 29: ASP, Nonterminal, was not found in name map.) (Residue 30: TYR, Nonterminal, was not found in name map.) (Residue 31: THR, Nonterminal, was not found in name map.) (Residue 32: SER, Nonterminal, was not found in name map.) (Residue 33: TYR, Nonterminal, was not found in name map.) (Residue 34: PHE, Nonterminal, was not found in name map.) (Residue 35: PRO, Nonterminal, was not found in name map.) (Residue 36: LYS, Nonterminal, was not found in name map.) (Residue 37: TYR, Nonterminal, was not found in name map.) (Residue 38: ALA, Nonterminal, was not found in name map.) (Residue 39: TYR, Nonterminal, was not found in name map.) (Residue 40: ARG, Nonterminal, was not found in name map.) (Residue 41: ASN, Nonterminal, was not found in name map.) (Residue 42: GLY, Nonterminal, was not found in name map.) (Residue 43: VAL, Nonterminal, was not found in name map.) (Residue 44: GLY, Nonterminal, was not found in name map.) (Residue 45: ARG, Nonterminal, was not found in name map.) (Residue 46: PRO, Nonterminal, was not found in name map.) (Residue 47: GLU, Nonterminal, was not found in name map.) (Residue 48: GLY, Nonterminal, was not found in name map.) (Residue 49: ILE, Nonterminal, was not found in name map.) (Residue 50: VAL, Nonterminal, was not found in name map.) (Residue 51: VAL, Nonterminal, was not found in name map.) (Residue 52: HIS, Nonterminal, was not found in name map.) (Residue 53: ASP, Nonterminal, was not found in name map.) (Residue 54: THR, Nonterminal, was not found in name map.) (Residue 55: ALA, Nonterminal, was not found in name map.) (Residue 56: ASN, Nonterminal, was not found in name map.) (Residue 57: ASP, Nonterminal, was not found in name map.) (Residue 58: ARG, Nonterminal, was not found in name map.) (Residue 59: SER, Nonterminal, was not found in name map.) (Residue 60: THR, Nonterminal, was not found in name map.) (Residue 61: ILE, Nonterminal, was not found in name map.) (Residue 62: ASN, Nonterminal, was not found in name map.) (Residue 63: GLY, Nonterminal, was not found in name map.) (Residue 64: GLU, Nonterminal, was not found in name map.) (Residue 65: ILE, Nonterminal, was not found in name map.) (Residue 66: SER, Nonterminal, was not found in name map.) (Residue 67: TYR, Nonterminal, was not found in name map.) (Residue 68: MET, Nonterminal, was not found in name map.) (Residue 69: LYS, Nonterminal, was not found in name map.) (Residue 70: ASN, Nonterminal, was not found in name map.) (Residue 71: ASN, Nonterminal, was not found in name map.) (Residue 72: TYR, Nonterminal, was not found in name map.) (Residue 73: GLN, Nonterminal, was not found in name map.) (Residue 74: ASN, Nonterminal, was not found in name map.) (Residue 75: ALA, Nonterminal, was not found in name map.) (Residue 76: PHE, Nonterminal, was not found in name map.) (Residue 77: VAL, Nonterminal, was not found in name map.) (Residue 78: HIS, Nonterminal, was not found in name map.) (Residue 79: ALA, Nonterminal, was not found in name map.) (Residue 80: PHE, Nonterminal, was not found in name map.) (Residue 81: VAL, Nonterminal, was not found in name map.) (Residue 82: ASP, Nonterminal, was not found in name map.) (Residue 83: GLY, Nonterminal, was not found in name map.) (Residue 84: ASP, Nonterminal, was not found in name map.) (Residue 85: ARG, Nonterminal, was not found in name map.) (Residue 86: ILE, Nonterminal, was not found in name map.) (Residue 87: ILE, Nonterminal, was not found in name map.) (Residue 88: GLU, Nonterminal, was not found in name map.) (Residue 89: THR, Nonterminal, was not found in name map.) (Residue 90: ALA, Nonterminal, was not found in name map.) (Residue 91: PRO, Nonterminal, was not found in name map.) (Residue 92: THR, Nonterminal, was not found in name map.) (Residue 93: ASP, Nonterminal, was not found in name map.) (Residue 94: TYR, Nonterminal, was not found in name map.) (Residue 95: LEU, Nonterminal, was not found in name map.) (Residue 96: SER, Nonterminal, was not found in name map.) (Residue 97: TRP, Nonterminal, was not found in name map.) (Residue 98: GLY, Nonterminal, was not found in name map.) (Residue 99: VAL, Nonterminal, was not found in name map.) (Residue 100: GLY, Nonterminal, was not found in name map.) (Residue 101: ALA, Nonterminal, was not found in name map.) (Residue 102: VAL, Nonterminal, was not found in name map.) (Residue 103: GLY, Nonterminal, was not found in name map.) (Residue 104: ASN, Nonterminal, was not found in name map.) (Residue 105: PRO, Nonterminal, was not found in name map.) (Residue 106: ARG, Nonterminal, was not found in name map.) (Residue 107: PHE, Nonterminal, was not found in name map.) (Residue 108: ILE, Nonterminal, was not found in name map.) (Residue 109: ASN, Nonterminal, was not found in name map.) (Residue 110: VAL, Nonterminal, was not found in name map.) (Residue 111: GLU, Nonterminal, was not found in name map.) (Residue 112: ILE, Nonterminal, was not found in name map.) (Residue 113: VAL, Nonterminal, was not found in name map.) (Residue 114: HIS, Nonterminal, was not found in name map.) (Residue 115: THR, Nonterminal, was not found in name map.) (Residue 116: HIS, Nonterminal, was not found in name map.) (Residue 117: ASP, Nonterminal, was not found in name map.) (Residue 118: TYR, Nonterminal, was not found in name map.) (Residue 119: ALA, Nonterminal, was not found in name map.) (Residue 120: SER, Nonterminal, was not found in name map.) (Residue 121: PHE, Nonterminal, was not found in name map.) (Residue 122: ALA, Nonterminal, was not found in name map.) (Residue 123: ARG, Nonterminal, was not found in name map.) (Residue 124: SER, Nonterminal, was not found in name map.) (Residue 125: MET, Nonterminal, was not found in name map.) (Residue 126: ASN, Nonterminal, was not found in name map.) (Residue 127: ASN, Nonterminal, was not found in name map.) (Residue 128: TYR, Nonterminal, was not found in name map.) (Residue 129: ALA, Nonterminal, was not found in name map.) (Residue 130: ASP, Nonterminal, was not found in name map.) (Residue 131: TYR, Nonterminal, was not found in name map.) (Residue 132: ALA, Nonterminal, was not found in name map.) (Residue 133: ALA, Nonterminal, was not found in name map.) (Residue 134: THR, Nonterminal, was not found in name map.) (Residue 135: GLN, Nonterminal, was not found in name map.) (Residue 136: LEU, Nonterminal, was not found in name map.) (Residue 137: GLN, Nonterminal, was not found in name map.) (Residue 138: TYR, Nonterminal, was not found in name map.) (Residue 139: TYR, Nonterminal, was not found in name map.) (Residue 140: GLY, Nonterminal, was not found in name map.) (Residue 141: LEU, Nonterminal, was not found in name map.) (Residue 142: LYS, Nonterminal, was not found in name map.) (Residue 143: PRO, Nonterminal, was not found in name map.) (Residue 144: ASP, Nonterminal, was not found in name map.) (Residue 145: SER, Nonterminal, was not found in name map.) (Residue 146: ALA, Nonterminal, was not found in name map.) (Residue 147: GLU, Nonterminal, was not found in name map.) (Residue 148: TYR, Nonterminal, was not found in name map.) (Residue 149: ASP, Nonterminal, was not found in name map.) (Residue 150: GLY, Nonterminal, was not found in name map.) (Residue 151: ASN, Nonterminal, was not found in name map.) (Residue 152: GLY, Nonterminal, was not found in name map.) (Residue 153: THR, Nonterminal, was not found in name map.) (Residue 154: VAL, Nonterminal, was not found in name map.) (Residue 155: TRP, Nonterminal, was not found in name map.) (Residue 156: THR, Nonterminal, was not found in name map.) (Residue 157: HIS, Nonterminal, was not found in name map.) (Residue 158: TYR, Nonterminal, was not found in name map.) (Residue 159: ALA, Nonterminal, was not found in name map.) (Residue 160: VAL, Nonterminal, was not found in name map.) (Residue 161: SER, Nonterminal, was not found in name map.) (Residue 162: LYS, Nonterminal, was not found in name map.) (Residue 163: TYR, Nonterminal, was not found in name map.) (Residue 164: LEU, Nonterminal, was not found in name map.) (Residue 165: GLY, Nonterminal, was not found in name map.) (Residue 166: GLY, Nonterminal, was not found in name map.) (Residue 167: THR, Nonterminal, was not found in name map.) (Residue 168: ASP, Nonterminal, was not found in name map.) (Residue 169: HIS, Nonterminal, was not found in name map.) (Residue 170: ALA, Nonterminal, was not found in name map.) (Residue 171: ASP, Nonterminal, was not found in name map.) (Residue 172: PRO, Nonterminal, was not found in name map.) (Residue 173: HIS, Nonterminal, was not found in name map.) (Residue 174: GLY, Nonterminal, was not found in name map.) (Residue 175: TYR, Nonterminal, was not found in name map.) (Residue 176: LEU, Nonterminal, was not found in name map.) (Residue 177: ARG, Nonterminal, was not found in name map.) (Residue 178: SER, Nonterminal, was not found in name map.) (Residue 179: HIS, Nonterminal, was not found in name map.) (Residue 180: ASN, Nonterminal, was not found in name map.) (Residue 181: TYR, Nonterminal, was not found in name map.) (Residue 182: SER, Nonterminal, was not found in name map.) (Residue 183: TYR, Nonterminal, was not found in name map.) (Residue 184: ASP, Nonterminal, was not found in name map.) (Residue 185: GLN, Nonterminal, was not found in name map.) (Residue 186: LEU, Nonterminal, was not found in name map.) (Residue 187: TYR, Nonterminal, was not found in name map.) (Residue 188: ASP, Nonterminal, was not found in name map.) (Residue 189: LEU, Nonterminal, was not found in name map.) (Residue 190: ILE, Nonterminal, was not found in name map.) (Residue 191: ASN, Nonterminal, was not found in name map.) (Residue 192: GLU, Nonterminal, was not found in name map.) (Residue 193: LYS, Nonterminal, was not found in name map.) (Residue 194: TYR, Nonterminal, was not found in name map.) (Residue 195: LEU, Nonterminal, was not found in name map.) (Residue 196: ILE, Nonterminal, was not found in name map.) (Residue 197: LYS, Nonterminal, was not found in name map.) (Residue 198: MET, Nonterminal, was not found in name map.) (Residue 199: GLY, Nonterminal, was not found in name map.) (Residue 200: LYS, Nonterminal, was not found in name map.) (Residue 201: VAL, Nonterminal, was not found in name map.) (Residue 202: ALA, Nonterminal, was not found in name map.) (Residue 203: PRO, Nonterminal, was not found in name map.) (Residue 204: TRP, Nonterminal, was not found in name map.) (Residue 205: GLY, Nonterminal, was not found in name map.) Mapped residue THR, term: Terminal/last, seq. number: 206 to: CTHR. (Residue 207: ZNB, Terminal/last, was not found in name map.) (Residue 208: HOH, Terminal/beginning, was not found in name map.) (Residue 209: HOH, Nonterminal, was not found in name map.) (Residue 210: HOH, Nonterminal, was not found in name map.) (Residue 211: HOH, Nonterminal, was not found in name map.) (Residue 212: HOH, Nonterminal, was not found in name map.) (Residue 213: HOH, Nonterminal, was not found in name map.) (Residue 214: HOH, Nonterminal, was not found in name map.) (Residue 215: HOH, Terminal/last, was not found in name map.) (Residue 216: HOH, Terminal/beginning, was not found in name map.) (Residue 217: HOH, Nonterminal, was not found in name map.) (Residue 218: HOH, Nonterminal, was not found in name map.) (Residue 219: HOH, Nonterminal, was not found in name map.) (Residue 220: HOH, Terminal/last, was not found in name map.) (Residue 221: PGN, Terminal/last, was not found in name map.) Joining NSER - LEU Joining LEU - PRO Joining PRO - LYS Joining LYS - TYR Joining TYR - LYS Joining LYS - PRO Joining PRO - GLN Joining GLN - VAL Joining VAL - ASN Joining ASN - SER Joining SER - SER Joining SER - ILE Joining ILE - ASN Joining ASN - ASP Joining ASP - TYR Joining TYR - ILE Joining ILE - CYS Joining CYS - LYS Joining LYS - ASN Joining ASN - ASN Joining ASN - LEU Joining LEU - LYS Joining LYS - ALA Joining ALA - PRO Joining PRO - LYS Joining LYS - ILE Joining ILE - GLU Joining GLU - GLU Joining GLU - ASP Joining ASP - TYR Joining TYR - THR Joining THR - SER Joining SER - TYR Joining TYR - PHE Joining PHE - PRO Joining PRO - LYS Joining LYS - TYR Joining TYR - ALA Joining ALA - TYR Joining TYR - ARG Joining ARG - ASN Joining ASN - GLY Joining GLY - VAL Joining VAL - GLY Joining GLY - ARG Joining ARG - PRO Joining PRO - GLU Joining GLU - GLY Joining GLY - ILE Joining ILE - VAL Joining VAL - VAL Joining VAL - HIE Joining HIE - ASP Joining ASP - THR Joining THR - ALA Joining ALA - ASN Joining ASN - ASP Joining ASP - ARG Joining ARG - SER Joining SER - THR Joining THR - ILE Joining ILE - ASN Joining ASN - GLY Joining GLY - GLU Joining GLU - ILE Joining ILE - SER Joining SER - TYR Joining TYR - MET Joining MET - LYS Joining LYS - ASN Joining ASN - ASN Joining ASN - TYR Joining TYR - GLN Joining GLN - ASN Joining ASN - ALA Joining ALA - PHE Joining PHE - VAL Joining VAL - HIE Joining HIE - ALA Joining ALA - PHE Joining PHE - VAL Joining VAL - ASP Joining ASP - GLY Joining GLY - ASP Joining ASP - ARG Joining ARG - ILE Joining ILE - ILE Joining ILE - GLU Joining GLU - THR Joining THR - ALA Joining ALA - PRO Joining PRO - THR Joining THR - ASP Joining ASP - TYR Joining TYR - LEU Joining LEU - SER Joining SER - TRP Joining TRP - GLY Joining GLY - VAL Joining VAL - GLY Joining GLY - ALA Joining ALA - VAL Joining VAL - GLY Joining GLY - ASN Joining ASN - PRO Joining PRO - ARG Joining ARG - PHE Joining PHE - ILE Joining ILE - ASN Joining ASN - VAL Joining VAL - GLU Joining GLU - ILE Joining ILE - VAL Joining VAL - HIE Joining HIE - THR Joining THR - HIE Joining HIE - ASP Joining ASP - TYR Joining TYR - ALA Joining ALA - SER Joining SER - PHE Joining PHE - ALA Joining ALA - ARG Joining ARG - SER Joining SER - MET Joining MET - ASN Joining ASN - ASN Joining ASN - TYR Joining TYR - ALA Joining ALA - ASP Joining ASP - TYR Joining TYR - ALA Joining ALA - ALA Joining ALA - THR Joining THR - GLN Joining GLN - LEU Joining LEU - GLN Joining GLN - TYR Joining TYR - TYR Joining TYR - GLY Joining GLY - LEU Joining LEU - LYS Joining LYS - PRO Joining PRO - ASP Joining ASP - SER Joining SER - ALA Joining ALA - GLU Joining GLU - TYR Joining TYR - ASP Joining ASP - GLY Joining GLY - ASN Joining ASN - GLY Joining GLY - THR Joining THR - VAL Joining VAL - TRP Joining TRP - THR Joining THR - HIE Joining HIE - TYR Joining TYR - ALA Joining ALA - VAL Joining VAL - SER Joining SER - LYS Joining LYS - TYR Joining TYR - LEU Joining LEU - GLY Joining GLY - GLY Joining GLY - THR Joining THR - ASP Joining ASP - HIE Joining HIE - ALA Joining ALA - ASP Joining ASP - PRO Joining PRO - HIE Joining HIE - GLY Joining GLY - TYR Joining TYR - LEU Joining LEU - ARG Joining ARG - SER Joining SER - HIE Joining HIE - ASN Joining ASN - TYR Joining TYR - SER Joining SER - TYR Joining TYR - ASP Joining ASP - GLN Joining GLN - LEU Joining LEU - TYR Joining TYR - ASP Joining ASP - LEU Joining LEU - ILE Joining ILE - ASN Joining ASN - GLU Joining GLU - LYS Joining LYS - TYR Joining TYR - LEU Joining LEU - ILE Joining ILE - LYS Joining LYS - MET Joining MET - GLY Joining GLY - LYS Joining LYS - VAL Joining VAL - ALA Joining ALA - PRO Joining PRO - TRP Joining TRP - GLY Joining GLY - CTHR Added missing heavy atom: .R.A Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 total atoms in file: 1730 Leap added 1642 missing atoms according to residue templates: 1 Heavy 1637 H / lone pairs 4 unknown element > saveamberparm com com.prmtop com.inpcrd Checking Unit. WARNING: The unperturbed charge of the unit: -1.999001 is not zero. WARNING: The perturbed charge: -1.999001 is not zero. -- ignoring the warnings. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. 1-4: angle 3229 3230 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3229 3230 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3229 3230 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3228 3229 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3228 3230 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3228 3229 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3228 3230 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3228 3229 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3228 3230 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3227 3228 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3227 3229 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3227 3230 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3227 3230 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3227 3229 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3227 3228 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3227 3230 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3227 3228 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3227 3229 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3226 3227 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3226 3230 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3226 3229 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3226 3228 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3226 3229 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3226 3230 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3226 3227 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3226 3228 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3226 3230 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3226 3227 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3226 3228 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3226 3229 duplicates bond ('triangular' bond) or angle ('square' bond) Building improper torsion parameters. ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 total 739 improper torsions applied Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected CTHR 1 NSER 1 PGN 1 WAT 13 ZNB 1 ) (no restraints)