> loadoff hiz.lib Loading library: ./hiz.lib Loading: HIZ > loadoff hia.lib Loading library: ./hia.lib Loading: HIA > loadoff hio.lib Loading library: ./hio.lib Loading: HIO > loadoff cym.lib Loading library: ./cym.lib Loading: CYM > loadoff cl.lib Loading library: ./cl.lib Loading: CL > NDM=loadpdb ndm-Zn.pdb Loading PDB file: ./ndm-Zn.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue LEU, term: Terminal/beginning, seq. number: 0 to: NLEU. (Residue 1: ASP, Nonterminal, was not found in name map.) (Residue 2: MET, Nonterminal, was not found in name map.) (Residue 3: PRO, Nonterminal, was not found in name map.) (Residue 4: GLY, Nonterminal, was not found in name map.) (Residue 5: PHE, Nonterminal, was not found in name map.) (Residue 6: GLY, Nonterminal, was not found in name map.) (Residue 7: ALA, Nonterminal, was not found in name map.) (Residue 8: VAL, Nonterminal, was not found in name map.) (Residue 9: ALA, Nonterminal, was not found in name map.) (Residue 10: SER, Nonterminal, was not found in name map.) (Residue 11: ASN, Nonterminal, was not found in name map.) (Residue 12: GLY, Nonterminal, was not found in name map.) (Residue 13: LEU, Nonterminal, was not found in name map.) (Residue 14: ILE, Nonterminal, was not found in name map.) (Residue 15: VAL, Nonterminal, was not found in name map.) (Residue 16: ARG, Nonterminal, was not found in name map.) (Residue 17: ASP, Nonterminal, was not found in name map.) (Residue 18: GLY, Nonterminal, was not found in name map.) (Residue 19: GLY, Nonterminal, was not found in name map.) (Residue 20: ARG, Nonterminal, was not found in name map.) (Residue 21: VAL, Nonterminal, was not found in name map.) (Residue 22: LEU, Nonterminal, was not found in name map.) (Residue 23: VAL, Nonterminal, was not found in name map.) (Residue 24: VAL, Nonterminal, was not found in name map.) (Residue 25: ASP, Nonterminal, was not found in name map.) (Residue 26: THR, Nonterminal, was not found in name map.) (Residue 27: ALA, Nonterminal, was not found in name map.) (Residue 28: TRP, Nonterminal, was not found in name map.) (Residue 29: THR, Nonterminal, was not found in name map.) (Residue 30: ASP, Nonterminal, was not found in name map.) (Residue 31: ASP, Nonterminal, was not found in name map.) (Residue 32: GLN, Nonterminal, was not found in name map.) (Residue 33: THR, Nonterminal, was not found in name map.) (Residue 34: ALA, Nonterminal, was not found in name map.) (Residue 35: GLN, Nonterminal, was not found in name map.) (Residue 36: ILE, Nonterminal, was not found in name map.) (Residue 37: LEU, Nonterminal, was not found in name map.) (Residue 38: ASN, Nonterminal, was not found in name map.) (Residue 39: TRP, Nonterminal, was not found in name map.) (Residue 40: ILE, Nonterminal, was not found in name map.) (Residue 41: LYS, Nonterminal, was not found in name map.) (Residue 42: GLN, Nonterminal, was not found in name map.) (Residue 43: GLU, Nonterminal, was not found in name map.) (Residue 44: ILE, Nonterminal, was not found in name map.) (Residue 45: ASN, Nonterminal, was not found in name map.) (Residue 46: LEU, Nonterminal, was not found in name map.) (Residue 47: PRO, Nonterminal, was not found in name map.) (Residue 48: VAL, Nonterminal, was not found in name map.) (Residue 49: ALA, Nonterminal, was not found in name map.) (Residue 50: LEU, Nonterminal, was not found in name map.) (Residue 51: ALA, Nonterminal, was not found in name map.) (Residue 52: VAL, Nonterminal, was not found in name map.) (Residue 53: VAL, Nonterminal, was not found in name map.) (Residue 54: THR, Nonterminal, was not found in name map.) (Residue 55: HIZ, Nonterminal, was not found in name map.) (Residue 56: ALA, Nonterminal, was not found in name map.) (Residue 57: HIE, Nonterminal, was not found in name map.) (Residue 58: GLN, Nonterminal, was not found in name map.) (Residue 59: ASP, Nonterminal, was not found in name map.) (Residue 60: LYS, Nonterminal, was not found in name map.) (Residue 61: MET, Nonterminal, was not found in name map.) (Residue 62: GLY, Nonterminal, was not found in name map.) (Residue 63: GLY, Nonterminal, was not found in name map.) (Residue 64: MET, Nonterminal, was not found in name map.) (Residue 65: ASP, Nonterminal, was not found in name map.) (Residue 66: ALA, Nonterminal, was not found in name map.) (Residue 67: LEU, Nonterminal, was not found in name map.) (Residue 68: HID, Nonterminal, was not found in name map.) (Residue 69: ALA, Nonterminal, was not found in name map.) (Residue 70: ALA, Nonterminal, was not found in name map.) (Residue 71: GLY, Nonterminal, was not found in name map.) (Residue 72: ILE, Nonterminal, was not found in name map.) (Residue 73: ALA, Nonterminal, was not found in name map.) (Residue 74: THR, Nonterminal, was not found in name map.) (Residue 75: TYR, Nonterminal, was not found in name map.) (Residue 76: ALA, Nonterminal, was not found in name map.) (Residue 77: ASN, Nonterminal, was not found in name map.) (Residue 78: ALA, Nonterminal, was not found in name map.) (Residue 79: LEU, Nonterminal, was not found in name map.) (Residue 80: SER, Nonterminal, was not found in name map.) (Residue 81: ASN, Nonterminal, was not found in name map.) (Residue 82: GLN, Nonterminal, was not found in name map.) (Residue 83: LEU, Nonterminal, was not found in name map.) (Residue 84: ALA, Nonterminal, was not found in name map.) (Residue 85: PRO, Nonterminal, was not found in name map.) (Residue 86: GLN, Nonterminal, was not found in name map.) (Residue 87: GLU, Nonterminal, was not found in name map.) (Residue 88: GLY, Nonterminal, was not found in name map.) (Residue 89: MET, Nonterminal, was not found in name map.) (Residue 90: VAL, Nonterminal, was not found in name map.) (Residue 91: ALA, Nonterminal, was not found in name map.) (Residue 92: ALA, Nonterminal, was not found in name map.) (Residue 93: GLN, Nonterminal, was not found in name map.) (Residue 94: HIA, Nonterminal, was not found in name map.) (Residue 95: SER, Nonterminal, was not found in name map.) (Residue 96: LEU, Nonterminal, was not found in name map.) (Residue 97: THR, Nonterminal, was not found in name map.) (Residue 98: PHE, Nonterminal, was not found in name map.) (Residue 99: ALA, Nonterminal, was not found in name map.) (Residue 100: ALA, Nonterminal, was not found in name map.) (Residue 101: ASN, Nonterminal, was not found in name map.) (Residue 102: GLY, Nonterminal, was not found in name map.) (Residue 103: TRP, Nonterminal, was not found in name map.) (Residue 104: VAL, Nonterminal, was not found in name map.) (Residue 105: GLU, Nonterminal, was not found in name map.) (Residue 106: PRO, Nonterminal, was not found in name map.) (Residue 107: ALA, Nonterminal, was not found in name map.) (Residue 108: THR, Nonterminal, was not found in name map.) (Residue 109: ALA, Nonterminal, was not found in name map.) (Residue 110: PRO, Nonterminal, was not found in name map.) (Residue 111: ASN, Nonterminal, was not found in name map.) (Residue 112: PHE, Nonterminal, was not found in name map.) (Residue 113: GLY, Nonterminal, was not found in name map.) (Residue 114: PRO, Nonterminal, was not found in name map.) (Residue 115: LEU, Nonterminal, was not found in name map.) (Residue 116: LYS, Nonterminal, was not found in name map.) (Residue 117: VAL, Nonterminal, was not found in name map.) (Residue 118: PHE, Nonterminal, was not found in name map.) (Residue 119: TYR, Nonterminal, was not found in name map.) (Residue 120: PRO, Nonterminal, was not found in name map.) (Residue 121: GLY, Nonterminal, was not found in name map.) (Residue 122: PRO, Nonterminal, was not found in name map.) (Residue 123: GLY, Nonterminal, was not found in name map.) (Residue 124: HIO, Nonterminal, was not found in name map.) (Residue 125: THR, Nonterminal, was not found in name map.) (Residue 126: SER, Nonterminal, was not found in name map.) (Residue 127: ASP, Nonterminal, was not found in name map.) (Residue 128: ASN, Nonterminal, was not found in name map.) (Residue 129: ILE, Nonterminal, was not found in name map.) (Residue 130: THR, Nonterminal, was not found in name map.) (Residue 131: VAL, Nonterminal, was not found in name map.) (Residue 132: GLY, Nonterminal, was not found in name map.) (Residue 133: ILE, Nonterminal, was not found in name map.) (Residue 134: ASP, Nonterminal, was not found in name map.) (Residue 135: GLY, Nonterminal, was not found in name map.) (Residue 136: THR, Nonterminal, was not found in name map.) (Residue 137: ASP, Nonterminal, was not found in name map.) (Residue 138: ILE, Nonterminal, was not found in name map.) (Residue 139: ALA, Nonterminal, was not found in name map.) (Residue 140: PHE, Nonterminal, was not found in name map.) (Residue 141: GLY, Nonterminal, was not found in name map.) (Residue 142: GLY, Nonterminal, was not found in name map.) (Residue 143: CYM, Nonterminal, was not found in name map.) (Residue 144: LEU, Nonterminal, was not found in name map.) (Residue 145: ILE, Nonterminal, was not found in name map.) (Residue 146: LYS, Nonterminal, was not found in name map.) (Residue 147: ASP, Nonterminal, was not found in name map.) (Residue 148: SER, Nonterminal, was not found in name map.) (Residue 149: LYS, Nonterminal, was not found in name map.) (Residue 150: ALA, Nonterminal, was not found in name map.) (Residue 151: LYS, Nonterminal, was not found in name map.) (Residue 152: SER, Nonterminal, was not found in name map.) (Residue 153: LEU, Nonterminal, was not found in name map.) (Residue 154: GLY, Nonterminal, was not found in name map.) (Residue 155: ASN, Nonterminal, was not found in name map.) (Residue 156: LEU, Nonterminal, was not found in name map.) (Residue 157: GLY, Nonterminal, was not found in name map.) (Residue 158: CL, Terminal/last, was not found in name map.) Joining NLEU - ASP Joining ASP - MET Joining MET - PRO Joining PRO - GLY Joining GLY - PHE Joining PHE - GLY Joining GLY - ALA Joining ALA - VAL Joining VAL - ALA Joining ALA - SER Joining SER - ASN Joining ASN - GLY Joining GLY - LEU Joining LEU - ILE Joining ILE - VAL Joining VAL - ARG Joining ARG - ASP Joining ASP - GLY Joining GLY - GLY Joining GLY - ARG Joining ARG - VAL Joining VAL - LEU Joining LEU - VAL Joining VAL - VAL Joining VAL - ASP Joining ASP - THR Joining THR - ALA Joining ALA - TRP Joining TRP - THR Joining THR - ASP Joining ASP - ASP Joining ASP - GLN Joining GLN - THR Joining THR - ALA Joining ALA - GLN Joining GLN - ILE Joining ILE - LEU Joining LEU - ASN Joining ASN - TRP Joining TRP - ILE Joining ILE - LYS Joining LYS - GLN Joining GLN - GLU Joining GLU - ILE Joining ILE - ASN Joining ASN - LEU Joining LEU - PRO Joining PRO - VAL Joining VAL - ALA Joining ALA - LEU Joining LEU - ALA Joining ALA - VAL Joining VAL - VAL Joining VAL - THR Joining THR - HIZ Joining HIZ - ALA Joining ALA - HIE Joining HIE - GLN Joining GLN - ASP Joining ASP - LYS Joining LYS - MET Joining MET - GLY Joining GLY - GLY Joining GLY - MET Joining MET - ASP Joining ASP - ALA Joining ALA - LEU Joining LEU - HID Joining HID - ALA Joining ALA - ALA Joining ALA - GLY Joining GLY - ILE Joining ILE - ALA Joining ALA - THR Joining THR - TYR Joining TYR - ALA Joining ALA - ASN Joining ASN - ALA Joining ALA - LEU Joining LEU - SER Joining SER - ASN Joining ASN - GLN Joining GLN - LEU Joining LEU - ALA Joining ALA - PRO Joining PRO - GLN Joining GLN - GLU Joining GLU - GLY Joining GLY - MET Joining MET - VAL Joining VAL - ALA Joining ALA - ALA Joining ALA - GLN Joining GLN - HIA Joining HIA - SER Joining SER - LEU Joining LEU - THR Joining THR - PHE Joining PHE - ALA Joining ALA - ALA Joining ALA - ASN Joining ASN - GLY Joining GLY - TRP Joining TRP - VAL Joining VAL - GLU Joining GLU - PRO Joining PRO - ALA Joining ALA - THR Joining THR - ALA Joining ALA - PRO Joining PRO - ASN Joining ASN - PHE Joining PHE - GLY Joining GLY - PRO Joining PRO - LEU Joining LEU - LYS Joining LYS - VAL Joining VAL - PHE Joining PHE - TYR Joining TYR - PRO Joining PRO - GLY Joining GLY - PRO Joining PRO - GLY Joining GLY - HIO Joining HIO - THR Joining THR - SER Joining SER - ASP Joining ASP - ASN Joining ASN - ILE Joining ILE - THR Joining THR - VAL Joining VAL - GLY Joining GLY - ILE Joining ILE - ASP Joining ASP - GLY Joining GLY - THR Joining THR - ASP Joining ASP - ILE Joining ILE - ALA Joining ALA - PHE Joining PHE - GLY Joining GLY - GLY Joining GLY - CYM Joining CYM - LEU Joining LEU - ILE Joining ILE - LYS Joining LYS - ASP Joining ASP - SER Joining SER - LYS Joining LYS - ALA Joining ALA - LYS Joining LYS - SER Joining SER - LEU Joining LEU - GLY Joining GLY - ASN Joining ASN - LEU Joining LEU - GLY One sided connection. Residue: missing connect0 atom. total atoms in file: 2294 > bond NDM.56.ZN NDM.58.ND1 > bond NDM.56.ZN NDM.125.OZ > bond NDM.56.ZN NDM.125.NE2 > bond NDM.144.ZN NDM.60.OD2 > bond NDM.144.ZN NDM.125.OZ > bond NDM.95.ZN NDM.95.OXI > bond NDM.95.ZN NDM.95.OIA > bond NDM.95.ZN NDM.95.OXA > solvateoct NDM TIP3PBOX 12 (using default radius 1.500000 for ZN) (using default radius 1.500000 for ZN) (using default radius 1.500000 for ZN) (using default radius 1.500000 for CL) Scaling up box by a factor of 1.363053 to meet diagonal cut criterion Solute vdw bounding box: 40.716 46.030 48.841 Total bounding box for atom centers: 81.554 81.554 81.554 (box expansion for 'iso' is 15.0%) Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 5 y= 5 z= 5 Adding box at: x=0 y=0 z=0 Center of solvent box is: 37.548698, 37.548698, 37.548698 Adding box at: x=0 y=0 z=1 Center of solvent box is: 37.548698, 37.548698, 18.774349 Adding box at: x=0 y=0 z=2 Center of solvent box is: 37.548698, 37.548698, 0.000000 Adding box at: x=0 y=0 z=3 Center of solvent box is: 37.548698, 37.548698, -18.774349 Adding box at: x=0 y=0 z=4 Center of solvent box is: 37.548698, 37.548698, -37.548698 Adding box at: x=0 y=1 z=0 Center of solvent box is: 37.548698, 18.774349, 37.548698 Adding box at: x=0 y=1 z=1 Center of solvent box is: 37.548698, 18.774349, 18.774349 Adding box at: x=0 y=1 z=2 Center of solvent box is: 37.548698, 18.774349, 0.000000 Adding box at: x=0 y=1 z=3 Center of solvent box is: 37.548698, 18.774349, -18.774349 Adding box at: x=0 y=1 z=4 Center of solvent box is: 37.548698, 18.774349, -37.548698 Adding box at: x=0 y=2 z=0 Center of solvent box is: 37.548698, 0.000000, 37.548698 Adding box at: x=0 y=2 z=1 Center of solvent box is: 37.548698, 0.000000, 18.774349 Adding box at: x=0 y=2 z=2 Center of solvent box is: 37.548698, 0.000000, 0.000000 Adding box at: x=0 y=2 z=3 Center of solvent box is: 37.548698, 0.000000, -18.774349 Adding box at: x=0 y=2 z=4 Center of solvent box is: 37.548698, 0.000000, -37.548698 Adding box at: x=0 y=3 z=0 Center of solvent box is: 37.548698, -18.774349, 37.548698 Adding box at: x=0 y=3 z=1 Center of solvent box is: 37.548698, -18.774349, 18.774349 Adding box at: x=0 y=3 z=2 Center of solvent box is: 37.548698, -18.774349, 0.000000 Adding box at: x=0 y=3 z=3 Center of solvent box is: 37.548698, -18.774349, -18.774349 Adding box at: x=0 y=3 z=4 Center of solvent box is: 37.548698, -18.774349, -37.548698 Adding box at: x=0 y=4 z=0 Center of solvent box is: 37.548698, -37.548698, 37.548698 Adding box at: x=0 y=4 z=1 Center of solvent box is: 37.548698, -37.548698, 18.774349 Adding box at: x=0 y=4 z=2 Center of solvent box is: 37.548698, -37.548698, 0.000000 Adding box at: x=0 y=4 z=3 Center of solvent box is: 37.548698, -37.548698, -18.774349 Adding box at: x=0 y=4 z=4 Center of solvent box is: 37.548698, -37.548698, -37.548698 Adding box at: x=1 y=0 z=0 Center of solvent box is: 18.774349, 37.548698, 37.548698 Adding box at: x=1 y=0 z=1 Center of solvent box is: 18.774349, 37.548698, 18.774349 Adding box at: x=1 y=0 z=2 Center of solvent box is: 18.774349, 37.548698, 0.000000 Adding box at: x=1 y=0 z=3 Center of solvent box is: 18.774349, 37.548698, -18.774349 Adding box at: x=1 y=0 z=4 Center of solvent box is: 18.774349, 37.548698, -37.548698 Adding box at: x=1 y=1 z=0 Center of solvent box is: 18.774349, 18.774349, 37.548698 Adding box at: x=1 y=1 z=1 Center of solvent box is: 18.774349, 18.774349, 18.774349 Adding box at: x=1 y=1 z=2 Center of solvent box is: 18.774349, 18.774349, 0.000000 Adding box at: x=1 y=1 z=3 Center of solvent box is: 18.774349, 18.774349, -18.774349 Adding box at: x=1 y=1 z=4 Center of solvent box is: 18.774349, 18.774349, -37.548698 Adding box at: x=1 y=2 z=0 Center of solvent box is: 18.774349, 0.000000, 37.548698 Adding box at: x=1 y=2 z=1 Center of solvent box is: 18.774349, 0.000000, 18.774349 Adding box at: x=1 y=2 z=2 Center of solvent box is: 18.774349, 0.000000, 0.000000 Adding box at: x=1 y=2 z=3 Center of solvent box is: 18.774349, 0.000000, -18.774349 Adding box at: x=1 y=2 z=4 Center of solvent box is: 18.774349, 0.000000, -37.548698 Adding box at: x=1 y=3 z=0 Center of solvent box is: 18.774349, -18.774349, 37.548698 Adding box at: x=1 y=3 z=1 Center of solvent box is: 18.774349, -18.774349, 18.774349 Adding box at: x=1 y=3 z=2 Center of solvent box is: 18.774349, -18.774349, 0.000000 Adding box at: x=1 y=3 z=3 Center of solvent box is: 18.774349, -18.774349, -18.774349 Adding box at: x=1 y=3 z=4 Center of solvent box is: 18.774349, -18.774349, -37.548698 Adding box at: x=1 y=4 z=0 Center of solvent box is: 18.774349, -37.548698, 37.548698 Adding box at: x=1 y=4 z=1 Center of solvent box is: 18.774349, -37.548698, 18.774349 Adding box at: x=1 y=4 z=2 Center of solvent box is: 18.774349, -37.548698, 0.000000 Adding box at: x=1 y=4 z=3 Center of solvent box is: 18.774349, -37.548698, -18.774349 Adding box at: x=1 y=4 z=4 Center of solvent box is: 18.774349, -37.548698, -37.548698 Adding box at: x=2 y=0 z=0 Center of solvent box is: 0.000000, 37.548698, 37.548698 Adding box at: x=2 y=0 z=1 Center of solvent box is: 0.000000, 37.548698, 18.774349 Adding box at: x=2 y=0 z=2 Center of solvent box is: 0.000000, 37.548698, 0.000000 Adding box at: x=2 y=0 z=3 Center of solvent box is: 0.000000, 37.548698, -18.774349 Adding box at: x=2 y=0 z=4 Center of solvent box is: 0.000000, 37.548698, -37.548698 Adding box at: x=2 y=1 z=0 Center of solvent box is: 0.000000, 18.774349, 37.548698 Adding box at: x=2 y=1 z=1 Center of solvent box is: 0.000000, 18.774349, 18.774349 Adding box at: x=2 y=1 z=2 Center of solvent box is: 0.000000, 18.774349, 0.000000 Adding box at: x=2 y=1 z=3 Center of solvent box is: 0.000000, 18.774349, -18.774349 Adding box at: x=2 y=1 z=4 Center of solvent box is: 0.000000, 18.774349, -37.548698 Adding box at: x=2 y=2 z=0 Center of solvent box is: 0.000000, 0.000000, 37.548698 Adding box at: x=2 y=2 z=1 Center of solvent box is: 0.000000, 0.000000, 18.774349 Adding box at: x=2 y=2 z=2 Center of solvent box is: 0.000000, 0.000000, 0.000000 Adding box at: x=2 y=2 z=3 Center of solvent box is: 0.000000, 0.000000, -18.774349 Adding box at: x=2 y=2 z=4 Center of solvent box is: 0.000000, 0.000000, -37.548698 Adding box at: x=2 y=3 z=0 Center of solvent box is: 0.000000, -18.774349, 37.548698 Adding box at: x=2 y=3 z=1 Center of solvent box is: 0.000000, -18.774349, 18.774349 Adding box at: x=2 y=3 z=2 Center of solvent box is: 0.000000, -18.774349, 0.000000 Adding box at: x=2 y=3 z=3 Center of solvent box is: 0.000000, -18.774349, -18.774349 Adding box at: x=2 y=3 z=4 Center of solvent box is: 0.000000, -18.774349, -37.548698 Adding box at: x=2 y=4 z=0 Center of solvent box is: 0.000000, -37.548698, 37.548698 Adding box at: x=2 y=4 z=1 Center of solvent box is: 0.000000, -37.548698, 18.774349 Adding box at: x=2 y=4 z=2 Center of solvent box is: 0.000000, -37.548698, 0.000000 Adding box at: x=2 y=4 z=3 Center of solvent box is: 0.000000, -37.548698, -18.774349 Adding box at: x=2 y=4 z=4 Center of solvent box is: 0.000000, -37.548698, -37.548698 Adding box at: x=3 y=0 z=0 Center of solvent box is: -18.774349, 37.548698, 37.548698 Adding box at: x=3 y=0 z=1 Center of solvent box is: -18.774349, 37.548698, 18.774349 Adding box at: x=3 y=0 z=2 Center of solvent box is: -18.774349, 37.548698, 0.000000 Adding box at: x=3 y=0 z=3 Center of solvent box is: -18.774349, 37.548698, -18.774349 Adding box at: x=3 y=0 z=4 Center of solvent box is: -18.774349, 37.548698, -37.548698 Adding box at: x=3 y=1 z=0 Center of solvent box is: -18.774349, 18.774349, 37.548698 Adding box at: x=3 y=1 z=1 Center of solvent box is: -18.774349, 18.774349, 18.774349 Adding box at: x=3 y=1 z=2 Center of solvent box is: -18.774349, 18.774349, 0.000000 Adding box at: x=3 y=1 z=3 Center of solvent box is: -18.774349, 18.774349, -18.774349 Adding box at: x=3 y=1 z=4 Center of solvent box is: -18.774349, 18.774349, -37.548698 Adding box at: x=3 y=2 z=0 Center of solvent box is: -18.774349, 0.000000, 37.548698 Adding box at: x=3 y=2 z=1 Center of solvent box is: -18.774349, 0.000000, 18.774349 Adding box at: x=3 y=2 z=2 Center of solvent box is: -18.774349, 0.000000, 0.000000 Adding box at: x=3 y=2 z=3 Center of solvent box is: -18.774349, 0.000000, -18.774349 Adding box at: x=3 y=2 z=4 Center of solvent box is: -18.774349, 0.000000, -37.548698 Adding box at: x=3 y=3 z=0 Center of solvent box is: -18.774349, -18.774349, 37.548698 Adding box at: x=3 y=3 z=1 Center of solvent box is: -18.774349, -18.774349, 18.774349 Adding box at: x=3 y=3 z=2 Center of solvent box is: -18.774349, -18.774349, 0.000000 Adding box at: x=3 y=3 z=3 Center of solvent box is: -18.774349, -18.774349, -18.774349 Adding box at: x=3 y=3 z=4 Center of solvent box is: -18.774349, -18.774349, -37.548698 Adding box at: x=3 y=4 z=0 Center of solvent box is: -18.774349, -37.548698, 37.548698 Adding box at: x=3 y=4 z=1 Center of solvent box is: -18.774349, -37.548698, 18.774349 Adding box at: x=3 y=4 z=2 Center of solvent box is: -18.774349, -37.548698, 0.000000 Adding box at: x=3 y=4 z=3 Center of solvent box is: -18.774349, -37.548698, -18.774349 Adding box at: x=3 y=4 z=4 Center of solvent box is: -18.774349, -37.548698, -37.548698 Adding box at: x=4 y=0 z=0 Center of solvent box is: -37.548698, 37.548698, 37.548698 Adding box at: x=4 y=0 z=1 Center of solvent box is: -37.548698, 37.548698, 18.774349 Adding box at: x=4 y=0 z=2 Center of solvent box is: -37.548698, 37.548698, 0.000000 Adding box at: x=4 y=0 z=3 Center of solvent box is: -37.548698, 37.548698, -18.774349 Adding box at: x=4 y=0 z=4 Center of solvent box is: -37.548698, 37.548698, -37.548698 Adding box at: x=4 y=1 z=0 Center of solvent box is: -37.548698, 18.774349, 37.548698 Adding box at: x=4 y=1 z=1 Center of solvent box is: -37.548698, 18.774349, 18.774349 Adding box at: x=4 y=1 z=2 Center of solvent box is: -37.548698, 18.774349, 0.000000 Adding box at: x=4 y=1 z=3 Center of solvent box is: -37.548698, 18.774349, -18.774349 Adding box at: x=4 y=1 z=4 Center of solvent box is: -37.548698, 18.774349, -37.548698 Adding box at: x=4 y=2 z=0 Center of solvent box is: -37.548698, 0.000000, 37.548698 Adding box at: x=4 y=2 z=1 Center of solvent box is: -37.548698, 0.000000, 18.774349 Adding box at: x=4 y=2 z=2 Center of solvent box is: -37.548698, 0.000000, 0.000000 Adding box at: x=4 y=2 z=3 Center of solvent box is: -37.548698, 0.000000, -18.774349 Adding box at: x=4 y=2 z=4 Center of solvent box is: -37.548698, 0.000000, -37.548698 Adding box at: x=4 y=3 z=0 Center of solvent box is: -37.548698, -18.774349, 37.548698 Adding box at: x=4 y=3 z=1 Center of solvent box is: -37.548698, -18.774349, 18.774349 Adding box at: x=4 y=3 z=2 Center of solvent box is: -37.548698, -18.774349, 0.000000 Adding box at: x=4 y=3 z=3 Center of solvent box is: -37.548698, -18.774349, -18.774349 Adding box at: x=4 y=3 z=4 Center of solvent box is: -37.548698, -18.774349, -37.548698 Adding box at: x=4 y=4 z=0 Center of solvent box is: -37.548698, -37.548698, 37.548698 Adding box at: x=4 y=4 z=1 Center of solvent box is: -37.548698, -37.548698, 18.774349 Adding box at: x=4 y=4 z=2 Center of solvent box is: -37.548698, -37.548698, 0.000000 Adding box at: x=4 y=4 z=3 Center of solvent box is: -37.548698, -37.548698, -18.774349 Adding box at: x=4 y=4 z=4 Center of solvent box is: -37.548698, -37.548698, -37.548698 (using default radius 1.500000 for ZN) (using default radius 1.500000 for ZN) (using default radius 1.500000 for ZN) (using default radius 1.500000 for CL) Volume: 281310.122 A^3 (oct) Mass > 150235.440 amu, Density > 0.887 g/cc (type - hence mass - of one or more atoms could not be found) Added 7425 residues. > charge NDM Total unperturbed charge: -5.000000 Total perturbed charge: -5.000000 > addions NDM Na+ 5 Adding 5 counter ions to "NDM" using 1A grid Used default radius 1.50 for 4 atoms Total solute charge: -5.00 Max atom radius: 2.00 Grid extends from solute vdw + 1.87 to 7.87 Box: enclosing: -27.50 -27.35 -25.00 30.51 30.03 31.12 sized: 36.50 36.65 39.00 edge: 64.00 Resolution: 1.00 Angstrom. Tree depth: 6 grid build: 0 sec Volume = 15.56% of box, grid points 40800 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 2 sec (Replacing solvent molecule) Placed Na+ in NDM at (-17.80, 7.00, -1.77). (Replacing solvent molecule) Placed Na+ in NDM at (-16.26, 11.24, 0.84). (Replacing solvent molecule) Placed Na+ in NDM at (20.83, -6.62, 2.67). (Replacing solvent molecule) Placed Na+ in NDM at (-21.48, -5.00, -3.01). (Replacing solvent molecule) Placed Na+ in NDM at (3.05, -12.79, -18.77). Done adding ions. > saveamberparm NDM ../results/ndm.prmtop ../results/ndm.inpcrd Checking Unit. WARNING: There is a bond of 3.592209 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 4.573484 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 3.280578 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 5.588924 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 3.528961 angstroms between: ------- .R.A and .R.A -- ignoring the warnings. Building topology. Building atom parameters. For atom: .R.A Could not find type: ZN For atom: .R.A Could not find type: ZN For atom: .R.A Could not find type: ZN For atom: .R.A Could not find type: CL Parameter file was not saved. > check NDM Checking 'NDM'.... WARNING: There is a bond of 3.592209 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 4.573484 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 3.280578 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 5.588924 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 3.528961 angstroms between: ------- .R.A and .R.A Warning: Close contact of 1.889165 angstroms between .R.A and .R.A Warning: Close contact of 2.139310 angstroms between .R.A and .R.A Warning: Close contact of 1.590002 angstroms between .R.A and .R.A Warning: Close contact of 0.974886 angstroms between .R.A and .R.A Warning: Close contact of 2.162066 angstroms between .R.A and .R.A Warning: Close contact of 1.781826 angstroms between .R.A and .R.A Warning: Close contact of 1.832578 angstroms between .R.A and .R.A Warning: Close contact of 1.643826 angstroms between .R.A and .R.A Warning: Close contact of 2.077037 angstroms between .R.A and .R.A Warning: Close contact of 2.005058 angstroms between .R.A and .R.A Warning: Close contact of 2.131461 angstroms between .R.A and .R.A Warning: Close contact of 0.668122 angstroms between .R.A and .R.A Warning: Close contact of 1.312491 angstroms between .R.A and .R.A Warning: Close contact of 1.425299 angstroms between .R.A and .R.A Warning: Close contact of 1.856501 angstroms between .R.A and .R.A Warning: Close contact of 1.160450 angstroms between .R.A and .R.A Warning: Close contact of 1.452026 angstroms between .R.A and .R.A Warning: Close contact of 2.054579 angstroms between .R.A and .R.A Warning: Close contact of 2.200242 angstroms between .R.A and .R.A Warning: Close contact of 1.345882 angstroms between .R.A and .R.A Warning: Close contact of 2.160977 angstroms between .R.A and .R.A Warning: Close contact of 1.879686 angstroms between .R.A and .R.A Warning: Close contact of 1.406442 angstroms between .R.A and .R.A Warning: Close contact of 2.073722 angstroms between .R.A and .R.A Warning: Close contact of 2.116182 angstroms between .R.A and .R.A Warning: Close contact of 2.127470 angstroms between .R.A and .R.A Warning: Close contact of 1.975830 angstroms between .R.A and .R.A Warning: Close contact of 2.047982 angstroms between .R.A and .R.A Warning: Close contact of 1.992814 angstroms between .R.A and .R.A Warning: Close contact of 1.474286 angstroms between .R.A and .R.A Checking parameters for unit 'NDM'. Checking for bond parameters. Could not find bond parameter for: ZN - NB No bond parameter for: ZN - NB Could not find bond parameter for: ZN - OW No bond parameter for: ZN - OW Could not find bond parameter for: ZN - NB No bond parameter for: ZN - NB Could not find bond parameter for: NB - ZN No bond parameter for: NB - ZN Could not find bond parameter for: O2 - ZN Could not find bond parameter for: ZN - OH No bond parameter for: ZN - OH Could not find bond parameter for: ZN - O No bond parameter for: ZN - O Could not find bond parameter for: ZN - OH No bond parameter for: ZN - OH Could not find bond parameter for: OW - ZN No bond parameter for: OW - ZN Could not find bond parameter for: SH - ZN Checking for angle parameters. Could not find angle parameter: ZN - NB - CC Can't find angle parameter: ZN - NB - CC Could not find angle parameter: ZN - NB - CR Can't find angle parameter: ZN - NB - CR Could not find angle parameter: ZN - OW - ZN Can't find angle parameter: ZN - OW - ZN Could not find angle parameter: ZN - NB - CR Can't find angle parameter: ZN - NB - CR Could not find angle parameter: ZN - NB - CV Can't find angle parameter: ZN - NB - CV Could not find angle parameter: CR - NB - ZN Can't find angle parameter: CR - NB - ZN Could not find angle parameter: CV - NB - ZN Can't find angle parameter: CV - NB - ZN Could not find angle parameter: NB - ZN - NB Can't find angle parameter: NB - ZN - NB Could not find angle parameter: NB - ZN - OW Can't find angle parameter: NB - ZN - OW Could not find angle parameter: NB - ZN - NB Can't find angle parameter: NB - ZN - NB Could not find angle parameter: NB - ZN - OW Can't find angle parameter: NB - ZN - OW Could not find angle parameter: NB - ZN - NB Can't find angle parameter: NB - ZN - NB Could not find angle parameter: O2 - ZN - SH Could not find angle parameter: O2 - ZN - OW Can't find angle parameter: O2 - ZN - OW Could not find angle parameter: C - O2 - ZN Could not find angle parameter: O - ZN - OH Can't find angle parameter: O - ZN - OH Could not find angle parameter: OH - ZN - O Can't find angle parameter: OH - ZN - O Could not find angle parameter: OH - ZN - OH Can't find angle parameter: OH - ZN - OH Could not find angle parameter: ZN - OH - C Can't find angle parameter: ZN - OH - C Could not find angle parameter: ZN - O - C Can't find angle parameter: ZN - O - C Could not find angle parameter: ZN - OH - C Can't find angle parameter: ZN - OH - C Could not find angle parameter: C - N - C Can't find angle parameter: C - N - C Could not find angle parameter: OW - ZN - SH Can't find angle parameter: OW - ZN - SH Could not find angle parameter: NB - ZN - OW Can't find angle parameter: NB - ZN - OW Could not find angle parameter: N - C - N Can't find angle parameter: N - C - N Could not find angle parameter: CT - SH - ZN There are missing parameters. check: Warnings: 35 Unit is OK. > saveoff NDM ndm.lib Creating ndm.lib Saving NDM. Building topology. Building atom parameters. > loadamberparams ndm-Zn.frcmod Loading parameters: ./ndm-Zn.frcmod Reading force field modification type file (frcmod) Reading title: # Zn parameters in AMBER forcefield for NDM-1 Unknown keyword: # from Ryd in parameter file. (UNKNOWN ATOM TYPE: ZN) > loadamberparams ndm-Zn.frcmod Loading parameters: ./ndm-Zn.frcmod Reading force field modification type file (frcmod) Reading title: # Zn parameters in AMBER forcefield for NDM-1 from Ryde 1995 and Dr. Walker's thesis (UNKNOWN ATOM TYPE: ZN) > saveamberparm NDM ../results/ndm.prmtop ../results/ndm.inpcrd Checking Unit. WARNING: There is a bond of 3.592209 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 4.573484 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 3.280578 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 5.588924 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 3.528961 angstroms between: ------- .R.A and .R.A -- ignoring the warnings. Building topology. Building atom parameters. For atom: .R.A Could not find type: CL Parameter file was not saved. > loadamberparams ndm-Zn.frcmod Loading parameters: ./ndm-Zn.frcmod Reading force field modification type file (frcmod) Reading title: # Zn parameters in AMBER forcefield for NDM-1 from Ryde 1995 and Dr. Walker's thesis (UNKNOWN ATOM TYPE: ZN) > saveamberparm NDM ../results/ndm.prmtop ../results/ndm.inpcrd Checking Unit. WARNING: There is a bond of 3.592209 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 4.573484 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 3.280578 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 5.588924 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 3.528961 angstroms between: ------- .R.A and .R.A -- ignoring the warnings. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Could not find angle parameter: O2 - ZN - SH Could not find angle parameter: ZN - O - C Building proper torsion parameters. 1-4: angle 1397 1398 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 1391 1396 duplicates bond ('triangular' bond) or angle ('square' bond) ** No torsion terms for ZN-OW-ZN-SH ** No torsion terms for ZN-OW-ZN-O2 ** No torsion terms for NB-ZN-OW-ZN ** No torsion terms for NB-ZN-OW-ZN ** No torsion terms for O2-C-O2-ZN ** No torsion terms for C-O2-ZN-SH ** No torsion terms for C-O2-ZN-OW ** No torsion terms for CT-C-O2-ZN ** No torsion terms for C-OH-ZN-O ** No torsion terms for OH-ZN-OH-C ** No torsion terms for C-OH-ZN-O ** No torsion terms for C-OH-ZN-OH ** No torsion terms for NB-ZN-OW-ZN 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 CR-CV-NB-ZN atoms are: CE1 CD2 NE2 ZN ** Warning: No sp2 improper torsion term for CC-CR-NB-ZN atoms are: CG CE1 ND1 ZN ** 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 N-CT-C-N atoms are: N CA C N ** Warning: No sp2 improper torsion term for CR-CV-NB-ZN atoms are: CE1 CD2 NE2 ZN total 455 improper torsions applied Building H-Bond parameters. Parameter file was not saved. > loadamberparams ndm-Zn.frcmod Loading parameters: ./ndm-Zn.frcmod Reading force field modification type file (frcmod) Reading title: # Zn parameters in AMBER forcefield for NDM-1 from Ryde 1995 and Dr. Walker's thesis (UNKNOWN ATOM TYPE: ZN) > saveamberparm NDM ../results/ndm.prmtop ../results/ndm.inpcrd Checking Unit. WARNING: There is a bond of 3.592209 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 4.573484 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 3.280578 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 5.588924 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 3.528961 angstroms between: ------- .R.A and .R.A -- ignoring the warnings. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. 1-4: angle 1397 1398 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 1391 1396 duplicates bond ('triangular' bond) or angle ('square' bond) ** No torsion terms for O2-C-O2-ZN ** No torsion terms for CT-C-O2-ZN 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 CR-CV-NB-ZN atoms are: CE1 CD2 NE2 ZN ** Warning: No sp2 improper torsion term for CC-CR-NB-ZN atoms are: CG CE1 ND1 ZN ** 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 N-CT-C-N atoms are: N CA C N ** Warning: No sp2 improper torsion term for CR-CV-NB-ZN atoms are: CE1 CD2 NE2 ZN total 455 improper torsions applied Building H-Bond parameters. Parameter file was not saved. > loadamberparams ndm-Zn.frcmod Loading parameters: ./ndm-Zn.frcmod Reading force field modification type file (frcmod) Reading title: # Zn parameters in AMBER forcefield for NDM-1 from Ryde 1995 and Dr. Walker's thesis (UNKNOWN ATOM TYPE: ZN) > saveamberparm NDM ../results/ndm.prmtop ../results/ndm.inpcrd Checking Unit. WARNING: There is a bond of 3.592209 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 4.573484 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 3.280578 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 5.588924 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 3.528961 angstroms between: ------- .R.A and .R.A -- ignoring the warnings. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. 1-4: angle 1397 1398 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 1391 1396 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 CR-CV-NB-ZN atoms are: CE1 CD2 NE2 ZN ** Warning: No sp2 improper torsion term for CC-CR-NB-ZN atoms are: CG CE1 ND1 ZN ** 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 N-CT-C-N atoms are: N CA C N ** Warning: No sp2 improper torsion term for CR-CV-NB-ZN atoms are: CE1 CD2 NE2 ZN total 455 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 HIA 1 HIO 1 HIZ 1 NLEU 1 WAT 7420 ) (no restraints) > quit