+------------------------------------------------------------------------------+ |____/\/\______/\/\__/\/\/\/\/\/\__/\/\____/\/\________________________________| |____/\/\/\__/\/\/\______/\/\______/\/\__/\/\________/\/\__________/\/\________| |____/\/\/\/\/\/\/\______/\/\______/\/\/\/\______/\/\/\/\/\/\__/\/\/\/\/\/\____| |____/\/\__/\__/\/\______/\/\______/\/\__/\/\________/\/\__________/\/\________| |____/\/\______/\/\______/\/\______/\/\____/\/\________________________________| +------------------------------------------------------------------------------+ | | | ____ ____ | | / \ / \ | | / \/ \ | | \ / | | \ / | | / \ | | / \ | | \ /\ / | | \____/ \____/ | | | | MTK++ 0.2.0 | | | | Copyright (C) 2005-2010 (see AUTHORS file for a list of contributors) | | | | MTK++ is free software; you can redistribute it and/or modify | | it under the terms of the GNU Lesser General Public License as published by | | the Free Software Foundation; either version 3 of the License, or | | (at your option) any later version. | | | | MTK++ is distributed in the hope that it will be useful, | | but WITHOUT ANY WARRANTY; without even the implied warranty of | | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | | GNU Lessser General Public License for more details. | | | | You should have received a copy of the GNU Lesser General Public License | | along with this program. If not, see . | | | +------------------------------------------------------------------------------+ | | | This program uses the MTK++ package. | | | +------------------------------------------------------------------------------+ | | | MCPB | | Martin B. Peters | | Copyright (c) 2005-2011 | | All Rights Reserved. | | | +------------------------------------------------------------------------------+ ### ### ### ### ### MTK++ Info ### ### Function: readInputFile ### ### Message: Commands read: source 3H68_OH_settings.bcl loadParam NAME_params_fc_md.xml loadLib NAME_stdMol.xml readPdb NAME NAME_fixed_H.pdb assignDisulfideBonds atomType assignConnectivity findMetalCenters writeLeap NAME NAME_mcpb.pdb writePdb NAME_mcpb.pdb quit ### ### ### ### ### ### ### ### ### MTK++ ### ### Function: elementParser ### ### Message: Reading XML with TINYXML ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: elementParser ### ### Message: Reading /Users/martin/Work/AMBER12/amber_28July2011/dat/mtkpp/elements.xml ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: readInputFile ### ### Message: Commands read: set NAME 3H68_OH set AMBERHOME /Users/martin/Work/AMBER12/amber_28July2011 loadParam AMBERHOME/dat/mtkpp/parm94.xml loadParam AMBERHOME/dat/mtkpp/parm_gaff.xml loadParam AMBERHOME/dat/mtkpp/metals/metalParm.xml loadParam caparm.xml loadLib AMBERHOME/dat/mtkpp/amino94.xml loadLib AMBERHOME/dat/mtkpp/aminont94.xml loadLib AMBERHOME/dat/mtkpp/aminoct94.xml loadLib AMBERHOME/dat/mtkpp/fragLib/terminal.xml loadLib AMBERHOME/dat/mtkpp/metals/metals.xml loadLib calib.xml ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: set ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: set ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: loadParam ### ### ### ### ### ### ### ### ### MTK++ ### ### Function: paramParser ### ### Message: Reading XML with TINYXML ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: paramParser ### ### Message: Reading /Users/martin/Work/AMBER12/amber_28July2011/dat/mtkpp/parm94.xml ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: loadParam ### ### ### ### ### ### ### ### ### MTK++ ### ### Function: paramParser ### ### Message: Reading XML with TINYXML ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: paramParser ### ### Message: Reading /Users/martin/Work/AMBER12/amber_28July2011/dat/mtkpp/parm_gaff.xml ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: loadParam ### ### ### ### ### ### ### ### ### MTK++ ### ### Function: paramParser ### ### Message: Reading XML with TINYXML ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: paramParser ### ### Message: Reading /Users/martin/Work/AMBER12/amber_28July2011/dat/mtkpp/metals/metalParm.xml ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: loadParam ### ### ### ### ### ### ### ### ### MTK++ ### ### Function: paramParser ### ### Message: Reading XML with TINYXML ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: paramParser ### ### Message: Reading caparm.xml ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: loadLib ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: stdLibParser ### ### Message: Reading /Users/martin/Work/AMBER12/amber_28July2011/dat/mtkpp/amino94.xml ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: loadLib ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: stdLibParser ### ### Message: Reading /Users/martin/Work/AMBER12/amber_28July2011/dat/mtkpp/aminont94.xml ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: loadLib ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: stdLibParser ### ### Message: Reading /Users/martin/Work/AMBER12/amber_28July2011/dat/mtkpp/aminoct94.xml ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: loadLib ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: stdLibParser ### ### Message: Reading /Users/martin/Work/AMBER12/amber_28July2011/dat/mtkpp/fragLib/terminal.xml ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: loadLib ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: stdLibParser ### ### Message: Reading /Users/martin/Work/AMBER12/amber_28July2011/dat/mtkpp/metals/metals.xml ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: loadLib ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: stdLibParser ### ### Message: Reading calib.xml ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: loadParam ### ### ### ### ### ### ### ### ### MTK++ ### ### Function: paramParser ### ### Message: Reading XML with TINYXML ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: paramParser ### ### Message: Reading 3H68_OH_params_fc_md.xml ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: loadLib ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: stdLibParser ### ### Message: Reading 3H68_OH_stdMol.xml ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: readPdb ### ### ### ### ### ### ### ### ### MTK++ Warning ### ### Function: pdbParser ### ### Message: Can't determine 1-letter code for CA1. Using 'X'. ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: assignDisulfideBonds ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: atomType ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: atomTyper::perceiveHistidines ### ### Message: Perceiving Histidine Residue Types HIS:30 Setting to HID HIS:121 Setting to HID HIS:123 Setting to HID HIS:129 Setting to HID HIS:263 Setting to HID HIS:288 Setting to HID HIS:299 Setting to HID HIS:306 Setting to HID ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: atomTyper::perceiveCysteines ### ### Message: Perceiving Cysteines Residue Types CYS:33 Setting to CYS CYS:65 Setting to CYS CYS:168 Setting to CYS CYS:207 Setting to CYS CYS:229 Setting to CYS CYS:267 Setting to CYS CYS:277 Setting to CYS ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: atomTyper::atomTypeByLib ### ### Message: Residue: 0 Assigned HD1 (l) Residue: 0 Assigned AS1 (l) Residue: 0 Assigned AS2 (l) Residue: 0 Assigned HD2 (l) Residue: 0 Assigned HE1 (l) Residue: 0 Assigned AN1 (l) Residue: 0 Assigned ZN1 (m) Residue: 0 Assigned ZN2 (m) Residue: 0 Assigned CA1 (m) ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: atomTyper::atomTypeByLib ### ### Message: Residue: 1 Assigned TYR (s) Residue: 2 Assigned SER (l) Residue: 3 Assigned GLY (l) Residue: 4 Assigned PRO (l) Residue: 5 Assigned LYS (l) Residue: 6 Assigned LEU (l) Residue: 7 Assigned GLU (l) Residue: 8 Assigned ASP (l) Residue: 9 Assigned GLY (l) Residue: 10 Assigned LYS (l) Residue: 11 Assigned VAL (l) Residue: 12 Assigned THR (l) Residue: 13 Assigned ILE (l) Residue: 14 Assigned SER (l) Residue: 15 Assigned PHE (l) Residue: 16 Assigned MET (l) Residue: 17 Assigned LYS (l) Residue: 18 Assigned GLU (l) Residue: 19 Assigned LEU (l) Residue: 20 Assigned MET (l) Residue: 21 Assigned GLN (l) Residue: 22 Assigned TRP (l) Residue: 23 Assigned TYR (l) Residue: 24 Assigned LYS (l) Residue: 25 Assigned ASP (l) Residue: 26 Assigned GLN (l) Residue: 27 Assigned LYS (l) Residue: 28 Assigned LYS (l) Residue: 29 Assigned LEU (l) Residue: 30 Assigned HID (l) Residue: 31 Assigned ARG (l) Residue: 32 Assigned LYS (l) Residue: 33 Assigned CYS (l) Residue: 34 Assigned ALA (l) Residue: 35 Assigned TYR (l) Residue: 36 Assigned GLN (l) Residue: 37 Assigned ILE (l) Residue: 38 Assigned LEU (l) Residue: 39 Assigned VAL (l) Residue: 40 Assigned GLN (l) Residue: 41 Assigned VAL (l) Residue: 42 Assigned LYS (l) Residue: 43 Assigned GLU (l) Residue: 44 Assigned VAL (l) Residue: 45 Assigned LEU (l) Residue: 46 Assigned SER (l) Residue: 47 Assigned LYS (l) Residue: 48 Assigned LEU (l) Residue: 49 Assigned SER (l) Residue: 50 Assigned THR (l) Residue: 51 Assigned LEU (l) Residue: 52 Assigned VAL (l) Residue: 53 Assigned GLU (l) Residue: 54 Assigned THR (l) Residue: 55 Assigned THR (l) Residue: 56 Assigned LEU (l) Residue: 57 Assigned LYS (l) Residue: 58 Assigned GLU (l) Residue: 59 Assigned THR (l) Residue: 60 Assigned GLU (l) Residue: 61 Assigned LYS (l) Residue: 62 Assigned ILE (l) Residue: 63 Assigned THR (l) Residue: 64 Assigned VAL (l) Residue: 65 Assigned CYS (l) Residue: 66 Assigned GLY (l) Residue: 67 Assigned ASP (l) Residue: 68 Assigned THR (l) Residue: 69 Assigned HID (l) Residue: 70 Assigned GLY (l) Residue: 71 Assigned GLN (l) Residue: 72 Assigned PHE (l) Residue: 73 Assigned TYR (l) Residue: 74 Assigned ASP (l) Residue: 75 Assigned LEU (l) Residue: 76 Assigned LEU (l) Residue: 77 Assigned ASN (l) Residue: 78 Assigned ILE (l) Residue: 79 Assigned PHE (l) Residue: 80 Assigned GLU (l) Residue: 81 Assigned LEU (l) Residue: 82 Assigned ASN (l) Residue: 83 Assigned GLY (l) Residue: 84 Assigned LEU (l) Residue: 85 Assigned PRO (l) Residue: 86 Assigned SER (l) Residue: 87 Assigned GLU (l) Residue: 88 Assigned THR (l) Residue: 89 Assigned ASN (l) Residue: 90 Assigned PRO (l) Residue: 91 Assigned TYR (l) Residue: 92 Assigned ILE (l) Residue: 93 Assigned PHE (l) Residue: 94 Assigned ASN (l) Residue: 95 Assigned GLY (l) Residue: 96 Assigned ASP (l) Residue: 97 Assigned PHE (l) Residue: 98 Assigned VAL (l) Residue: 99 Assigned ASP (l) Residue: 100 Assigned ARG (l) Residue: 101 Assigned GLY (l) Residue: 102 Assigned SER (l) Residue: 103 Assigned PHE (l) Residue: 104 Assigned SER (l) Residue: 105 Assigned VAL (l) Residue: 106 Assigned GLU (l) Residue: 107 Assigned VAL (l) Residue: 108 Assigned ILE (l) Residue: 109 Assigned LEU (l) Residue: 110 Assigned THR (l) Residue: 111 Assigned LEU (l) Residue: 112 Assigned PHE (l) Residue: 113 Assigned GLY (l) Residue: 114 Assigned PHE (l) Residue: 115 Assigned LYS (l) Residue: 116 Assigned LEU (l) Residue: 117 Assigned LEU (l) Residue: 118 Assigned TYR (l) Residue: 119 Assigned PRO (l) Residue: 120 Assigned ASP (l) Residue: 121 Assigned HID (l) Residue: 122 Assigned PHE (l) Residue: 123 Assigned HID (l) Residue: 124 Assigned LEU (l) Residue: 125 Assigned LEU (l) Residue: 126 Assigned ARG (l) Residue: 127 Assigned GLY (l) Residue: 128 Assigned ASN (l) Residue: 129 Assigned HID (l) Residue: 130 Assigned GLU (l) Residue: 131 Assigned THR (l) Residue: 132 Assigned ASP (l) Residue: 133 Assigned ASN (l) Residue: 134 Assigned MET (l) Residue: 135 Assigned ASN (l) Residue: 136 Assigned GLN (l) Residue: 137 Assigned ILE (l) Residue: 138 Assigned TYR (l) Residue: 139 Assigned GLY (l) Residue: 140 Assigned PHE (l) Residue: 141 Assigned GLU (l) Residue: 142 Assigned GLY (l) Residue: 143 Assigned GLU (l) Residue: 144 Assigned VAL (l) Residue: 145 Assigned LYS (l) Residue: 146 Assigned ALA (l) Residue: 147 Assigned LYS (l) Residue: 148 Assigned TYR (l) Residue: 149 Assigned THR (l) Residue: 150 Assigned ALA (l) Residue: 151 Assigned GLN (l) Residue: 152 Assigned MET (l) Residue: 153 Assigned TYR (l) Residue: 154 Assigned GLU (l) Residue: 155 Assigned LEU (l) Residue: 156 Assigned PHE (l) Residue: 157 Assigned SER (l) Residue: 158 Assigned GLU (l) Residue: 159 Assigned VAL (l) Residue: 160 Assigned PHE (l) Residue: 161 Assigned GLU (l) Residue: 162 Assigned TRP (l) Residue: 163 Assigned LEU (l) Residue: 164 Assigned PRO (l) Residue: 165 Assigned LEU (l) Residue: 166 Assigned ALA (l) Residue: 167 Assigned GLN (l) Residue: 168 Assigned CYS (l) Residue: 169 Assigned ILE (l) Residue: 170 Assigned ASN (l) Residue: 171 Assigned GLY (l) Residue: 172 Assigned LYS (l) Residue: 173 Assigned VAL (l) Residue: 174 Assigned LEU (l) Residue: 175 Assigned ILE (l) Residue: 176 Assigned MET (l) Residue: 177 Assigned HID (l) Residue: 178 Assigned GLY (l) Residue: 179 Assigned GLY (l) Residue: 180 Assigned LEU (l) Residue: 181 Assigned PHE (l) Residue: 182 Assigned SER (l) Residue: 183 Assigned GLU (l) Residue: 184 Assigned ASP (l) Residue: 185 Assigned GLY (l) Residue: 186 Assigned VAL (l) Residue: 187 Assigned THR (l) Residue: 188 Assigned LEU (l) Residue: 189 Assigned ASP (l) Residue: 190 Assigned ASP (l) Residue: 191 Assigned ILE (l) Residue: 192 Assigned ARG (l) Residue: 193 Assigned LYS (l) Residue: 194 Assigned ILE (l) Residue: 195 Assigned GLU (l) Residue: 196 Assigned ARG (l) Residue: 197 Assigned ASN (l) Residue: 198 Assigned ARG (l) Residue: 199 Assigned GLN (l) Residue: 200 Assigned PRO (l) Residue: 201 Assigned PRO (l) Residue: 202 Assigned ASP (l) Residue: 203 Assigned SER (l) Residue: 204 Assigned GLY (l) Residue: 205 Assigned PRO (l) Residue: 206 Assigned MET (l) Residue: 207 Assigned CYS (l) Residue: 208 Assigned ASP (l) Residue: 209 Assigned LEU (l) Residue: 210 Assigned LEU (l) Residue: 211 Assigned TRP (l) Residue: 212 Assigned SER (l) Residue: 213 Assigned ASP (l) Residue: 214 Assigned PRO (l) Residue: 215 Assigned GLN (l) Residue: 216 Assigned PRO (l) Residue: 217 Assigned GLN (l) Residue: 218 Assigned ASN (l) Residue: 219 Assigned GLY (l) Residue: 220 Assigned ARG (l) Residue: 221 Assigned SER (l) Residue: 222 Assigned ILE (l) Residue: 223 Assigned SER (l) Residue: 224 Assigned LYS (l) Residue: 225 Assigned ARG (l) Residue: 226 Assigned GLY (l) Residue: 227 Assigned VAL (l) Residue: 228 Assigned SER (l) Residue: 229 Assigned CYS (l) Residue: 230 Assigned GLN (l) Residue: 231 Assigned PHE (l) Residue: 232 Assigned GLY (l) Residue: 233 Assigned PRO (l) Residue: 234 Assigned ASP (l) Residue: 235 Assigned VAL (l) Residue: 236 Assigned THR (l) Residue: 237 Assigned LYS (l) Residue: 238 Assigned ALA (l) Residue: 239 Assigned PHE (l) Residue: 240 Assigned LEU (l) Residue: 241 Assigned GLU (l) Residue: 242 Assigned GLU (l) Residue: 243 Assigned ASN (l) Residue: 244 Assigned ASN (l) Residue: 245 Assigned LEU (l) Residue: 246 Assigned ASP (l) Residue: 247 Assigned TYR (l) Residue: 248 Assigned ILE (l) Residue: 249 Assigned ILE (l) Residue: 250 Assigned ARG (l) Residue: 251 Assigned SER (l) Residue: 252 Assigned HIE (l) Residue: 253 Assigned GLU (l) Residue: 254 Assigned VAL (l) Residue: 255 Assigned LYS (l) Residue: 256 Assigned ALA (l) Residue: 257 Assigned GLU (l) Residue: 258 Assigned GLY (l) Residue: 259 Assigned TYR (l) Residue: 260 Assigned GLU (l) Residue: 261 Assigned VAL (l) Residue: 262 Assigned ALA (l) Residue: 263 Assigned HID (l) Residue: 264 Assigned GLY (l) Residue: 265 Assigned GLY (l) Residue: 266 Assigned ARG (l) Residue: 267 Assigned CYS (l) Residue: 268 Assigned VAL (l) Residue: 269 Assigned THR (l) Residue: 270 Assigned VAL (l) Residue: 271 Assigned PHE (l) Residue: 272 Assigned SER (l) Residue: 273 Assigned ALA (l) Residue: 274 Assigned PRO (l) Residue: 275 Assigned ASN (l) Residue: 276 Assigned TYR (l) Residue: 277 Assigned CYS (l) Residue: 278 Assigned ASP (l) Residue: 279 Assigned GLN (l) Residue: 280 Assigned MET (l) Residue: 281 Assigned GLY (l) Residue: 282 Assigned ASN (l) Residue: 283 Assigned LYS (l) Residue: 284 Assigned ALA (l) Residue: 285 Assigned SER (l) Residue: 286 Assigned TYR (l) Residue: 287 Assigned ILE (l) Residue: 288 Assigned HID (l) Residue: 289 Assigned LEU (l) Residue: 290 Assigned GLN (l) Residue: 291 Assigned GLY (l) Residue: 292 Assigned SER (l) Residue: 293 Assigned ASP (l) Residue: 294 Assigned LEU (l) Residue: 295 Assigned ARG (l) Residue: 296 Assigned PRO (l) Residue: 297 Assigned GLN (l) Residue: 298 Assigned PHE (l) Residue: 299 Assigned HID (l) Residue: 300 Assigned GLN (l) Residue: 301 Assigned PHE (l) Residue: 302 Assigned THR (l) Residue: 303 Assigned ALA (l) Residue: 304 Assigned VAL (l) Residue: 305 Assigned PRO (l) Residue: 306 Assigned HID (l) Residue: 307 Assigned PRO (l) Residue: 308 Assigned ASN (l) Residue: 309 Assigned VAL (l) Residue: 310 Assigned LYS (l) Residue: 311 Assigned PRO (l) Residue: 312 Assigned MET (l) Residue: 313 Assigned ALA (l) Residue: 314 Assigned TYR (l) Residue: 315 Assigned ALA (e) ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: atomTyper::atomTypeByLib ### ### Message: Residue: 316 Assigned ZN (m) ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: atomTyper::atomTypeByLib ### ### Message: Residue: 317 Assigned ZN (m) ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: atomTyper::atomTypeByLib ### ### Message: Residue: 318 Assigned CA1 (m) ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: assignConnectivity ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::run ### ### Message: Collection Begin ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignBonds ### ### Message: Molecule Begin # 0 HD1: 0 bonds were added. AS1: 0 bonds were added. AS2: 0 bonds were added. HD2: 0 bonds were added. HE1: 0 bonds were added. AN1: 0 bonds were added. ZN1: 0 bonds were added. ZN2: 0 bonds were added. CA1: 0 bonds were added. ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignBonds ### ### Message: Molecule Begin # 1 TYR: 23 bonds were added. SER: 11 bonds were added. GLY: 7 bonds were added. PRO: 15 bonds were added. LYS: 22 bonds were added. LEU: 19 bonds were added. GLU: 15 bonds were added. ASP: 12 bonds were added. GLY: 7 bonds were added. LYS: 22 bonds were added. VAL: 16 bonds were added. THR: 14 bonds were added. ILE: 19 bonds were added. SER: 11 bonds were added. PHE: 21 bonds were added. MET: 17 bonds were added. LYS: 22 bonds were added. GLU: 15 bonds were added. LEU: 19 bonds were added. MET: 17 bonds were added. GLN: 17 bonds were added. TRP: 26 bonds were added. TYR: 22 bonds were added. LYS: 22 bonds were added. ASP: 12 bonds were added. GLN: 17 bonds were added. LYS: 22 bonds were added. LYS: 22 bonds were added. LEU: 19 bonds were added. HID: 18 bonds were added. ARG: 24 bonds were added. LYS: 22 bonds were added. CYS: 11 bonds were added. ALA: 10 bonds were added. TYR: 22 bonds were added. GLN: 17 bonds were added. ILE: 19 bonds were added. LEU: 19 bonds were added. VAL: 16 bonds were added. GLN: 17 bonds were added. VAL: 16 bonds were added. LYS: 22 bonds were added. GLU: 15 bonds were added. VAL: 16 bonds were added. LEU: 19 bonds were added. SER: 11 bonds were added. LYS: 22 bonds were added. LEU: 19 bonds were added. SER: 11 bonds were added. THR: 14 bonds were added. LEU: 19 bonds were added. VAL: 16 bonds were added. GLU: 15 bonds were added. THR: 14 bonds were added. THR: 14 bonds were added. LEU: 19 bonds were added. LYS: 22 bonds were added. GLU: 15 bonds were added. THR: 14 bonds were added. GLU: 15 bonds were added. LYS: 22 bonds were added. ILE: 19 bonds were added. THR: 14 bonds were added. VAL: 16 bonds were added. CYS: 11 bonds were added. GLY: 7 bonds were added. ASP: 12 bonds were added. THR: 14 bonds were added. HID: 18 bonds were added. GLY: 7 bonds were added. GLN: 17 bonds were added. PHE: 21 bonds were added. TYR: 22 bonds were added. ASP: 12 bonds were added. LEU: 19 bonds were added. LEU: 19 bonds were added. ASN: 14 bonds were added. ILE: 19 bonds were added. PHE: 21 bonds were added. GLU: 15 bonds were added. LEU: 19 bonds were added. ASN: 14 bonds were added. GLY: 7 bonds were added. LEU: 19 bonds were added. PRO: 15 bonds were added. SER: 11 bonds were added. GLU: 15 bonds were added. THR: 14 bonds were added. ASN: 14 bonds were added. PRO: 15 bonds were added. TYR: 22 bonds were added. ILE: 19 bonds were added. PHE: 21 bonds were added. ASN: 14 bonds were added. GLY: 7 bonds were added. ASP: 12 bonds were added. PHE: 21 bonds were added. VAL: 16 bonds were added. ASP: 12 bonds were added. ARG: 24 bonds were added. GLY: 7 bonds were added. SER: 11 bonds were added. PHE: 21 bonds were added. SER: 11 bonds were added. VAL: 16 bonds were added. GLU: 15 bonds were added. VAL: 16 bonds were added. ILE: 19 bonds were added. LEU: 19 bonds were added. THR: 14 bonds were added. LEU: 19 bonds were added. PHE: 21 bonds were added. GLY: 7 bonds were added. PHE: 21 bonds were added. LYS: 22 bonds were added. LEU: 19 bonds were added. LEU: 19 bonds were added. TYR: 22 bonds were added. PRO: 15 bonds were added. ASP: 12 bonds were added. HID: 18 bonds were added. PHE: 21 bonds were added. HID: 18 bonds were added. LEU: 19 bonds were added. LEU: 19 bonds were added. ARG: 24 bonds were added. GLY: 7 bonds were added. ASN: 14 bonds were added. HID: 18 bonds were added. GLU: 15 bonds were added. THR: 14 bonds were added. ASP: 12 bonds were added. ASN: 14 bonds were added. MET: 17 bonds were added. ASN: 14 bonds were added. GLN: 17 bonds were added. ILE: 19 bonds were added. TYR: 22 bonds were added. GLY: 7 bonds were added. PHE: 21 bonds were added. GLU: 15 bonds were added. GLY: 7 bonds were added. GLU: 15 bonds were added. VAL: 16 bonds were added. LYS: 22 bonds were added. ALA: 10 bonds were added. LYS: 22 bonds were added. TYR: 22 bonds were added. THR: 14 bonds were added. ALA: 10 bonds were added. GLN: 17 bonds were added. MET: 17 bonds were added. TYR: 22 bonds were added. GLU: 15 bonds were added. LEU: 19 bonds were added. PHE: 21 bonds were added. SER: 11 bonds were added. GLU: 15 bonds were added. VAL: 16 bonds were added. PHE: 21 bonds were added. GLU: 15 bonds were added. TRP: 26 bonds were added. LEU: 19 bonds were added. PRO: 15 bonds were added. LEU: 19 bonds were added. ALA: 10 bonds were added. GLN: 17 bonds were added. CYS: 11 bonds were added. ILE: 19 bonds were added. ASN: 14 bonds were added. GLY: 7 bonds were added. LYS: 22 bonds were added. VAL: 16 bonds were added. LEU: 19 bonds were added. ILE: 19 bonds were added. MET: 17 bonds were added. HID: 18 bonds were added. GLY: 7 bonds were added. GLY: 7 bonds were added. LEU: 19 bonds were added. PHE: 21 bonds were added. SER: 11 bonds were added. GLU: 15 bonds were added. ASP: 12 bonds were added. GLY: 7 bonds were added. VAL: 16 bonds were added. THR: 14 bonds were added. LEU: 19 bonds were added. ASP: 12 bonds were added. ASP: 12 bonds were added. ILE: 19 bonds were added. ARG: 24 bonds were added. LYS: 22 bonds were added. ILE: 19 bonds were added. GLU: 15 bonds were added. ARG: 24 bonds were added. ASN: 14 bonds were added. ARG: 24 bonds were added. GLN: 17 bonds were added. PRO: 15 bonds were added. PRO: 15 bonds were added. ASP: 12 bonds were added. SER: 11 bonds were added. GLY: 7 bonds were added. PRO: 15 bonds were added. MET: 17 bonds were added. CYS: 11 bonds were added. ASP: 12 bonds were added. LEU: 19 bonds were added. LEU: 19 bonds were added. TRP: 26 bonds were added. SER: 11 bonds were added. ASP: 12 bonds were added. PRO: 15 bonds were added. GLN: 17 bonds were added. PRO: 15 bonds were added. GLN: 17 bonds were added. ASN: 14 bonds were added. GLY: 7 bonds were added. ARG: 24 bonds were added. SER: 11 bonds were added. ILE: 19 bonds were added. SER: 11 bonds were added. LYS: 22 bonds were added. ARG: 24 bonds were added. GLY: 7 bonds were added. VAL: 16 bonds were added. SER: 11 bonds were added. CYS: 11 bonds were added. GLN: 17 bonds were added. PHE: 21 bonds were added. GLY: 7 bonds were added. PRO: 15 bonds were added. ASP: 12 bonds were added. VAL: 16 bonds were added. THR: 14 bonds were added. LYS: 22 bonds were added. ALA: 10 bonds were added. PHE: 21 bonds were added. LEU: 19 bonds were added. GLU: 15 bonds were added. GLU: 15 bonds were added. ASN: 14 bonds were added. ASN: 14 bonds were added. LEU: 19 bonds were added. ASP: 12 bonds were added. TYR: 22 bonds were added. ILE: 19 bonds were added. ILE: 19 bonds were added. ARG: 24 bonds were added. SER: 11 bonds were added. HIE: 18 bonds were added. GLU: 15 bonds were added. VAL: 16 bonds were added. LYS: 22 bonds were added. ALA: 10 bonds were added. GLU: 15 bonds were added. GLY: 7 bonds were added. TYR: 22 bonds were added. GLU: 15 bonds were added. VAL: 16 bonds were added. ALA: 10 bonds were added. HID: 18 bonds were added. GLY: 7 bonds were added. GLY: 7 bonds were added. ARG: 24 bonds were added. CYS: 11 bonds were added. VAL: 16 bonds were added. THR: 14 bonds were added. VAL: 16 bonds were added. PHE: 21 bonds were added. SER: 11 bonds were added. ALA: 10 bonds were added. PRO: 15 bonds were added. ASN: 14 bonds were added. TYR: 22 bonds were added. CYS: 11 bonds were added. ASP: 12 bonds were added. GLN: 17 bonds were added. MET: 17 bonds were added. GLY: 7 bonds were added. ASN: 14 bonds were added. LYS: 22 bonds were added. ALA: 10 bonds were added. SER: 11 bonds were added. TYR: 22 bonds were added. ILE: 19 bonds were added. HID: 18 bonds were added. LEU: 19 bonds were added. GLN: 17 bonds were added. GLY: 7 bonds were added. SER: 11 bonds were added. ASP: 12 bonds were added. LEU: 19 bonds were added. ARG: 24 bonds were added. PRO: 15 bonds were added. GLN: 17 bonds were added. PHE: 21 bonds were added. HID: 18 bonds were added. GLN: 17 bonds were added. PHE: 21 bonds were added. THR: 14 bonds were added. ALA: 10 bonds were added. VAL: 16 bonds were added. PRO: 15 bonds were added. HID: 18 bonds were added. PRO: 15 bonds were added. ASN: 14 bonds were added. VAL: 16 bonds were added. LYS: 22 bonds were added. PRO: 15 bonds were added. MET: 17 bonds were added. ALA: 10 bonds were added. TYR: 22 bonds were added. ALA: 11 bonds were added. ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignBonds ### ### Message: Molecule Begin # 2 ZN: 0 bonds were added. ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignBonds ### ### Message: Molecule Begin # 3 ZN: 0 bonds were added. ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignBonds ### ### Message: Molecule Begin # 4 CA1: 28 bonds were added. ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignAngles ### ### Message: Molecule # 0 0 angles were added ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignAngles ### ### Message: Molecule # 1 9133 angles were added ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignAngles ### ### Message: Molecule # 2 0 angles were added ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignAngles ### ### Message: Molecule # 3 0 angles were added ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignAngles ### ### Message: Molecule # 4 55 angles were added ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignTorsions ### ### Message: Molecule # 0 ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignTorsions ### ### Message: 0 torsions were added ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignTorsions ### ### Message: Molecule # 1 ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignTorsions ### ### Message: 13422 torsions were added ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignTorsions ### ### Message: Molecule # 2 ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignTorsions ### ### Message: 0 torsions were added ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignTorsions ### ### Message: Molecule # 3 ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignTorsions ### ### Message: 0 torsions were added ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignTorsions ### ### Message: Molecule # 4 ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignTorsions ### ### Message: 90 torsions were added ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignImpropers ### ### Message: Molecule # 0 ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignImpropers ### ### Message: Molecule # 1 ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignImpropers ### ### Message: Molecule # 2 ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignImpropers ### ### Message: Molecule # 3 ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignImpropers ### ### Message: Molecule # 4 ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignStdBonds ### ### Message: Collection Begin ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignStdBonds ### ### Message: Molecule # 0 ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignStdBonds ### ### Message: Molecule # 1 ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignStdBonds ### ### Message: Molecule # 2 ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignStdBonds ### ### Message: Molecule # 3 ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignStdBonds ### ### Message: Molecule # 4 ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignStdAngles ### ### Message: Collection Begin ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignStdAngles ### ### Message: Molecule # 0 ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignStdAngles ### ### Message: Molecule # 1 ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignStdAngles ### ### Message: Molecule # 2 ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignStdAngles ### ### Message: Molecule # 3 ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignStdAngles ### ### Message: Molecule # 4 ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignStdTorsions ### ### Message: Collection Begin ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignStdTorsions ### ### Message: Molecule # 0 ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignStdTorsions ### ### Message: Molecule # 1 ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignStdTorsions ### ### Message: Molecule # 2 ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignStdTorsions ### ### Message: Molecule # 3 ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignStdTorsions ### ### Message: Molecule # 4 ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: findMetalCenters ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB::findMetalCenters ### ### Message: Start ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: collection::hasMetal ### ### Message: Found Metal: Zn ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: collection::findMetals ### ### Message: Metal Found: Zn:4995 Zn:4996 ### ### ### ### ### ### ### ### ### MTK++ Warning ### ### Function: stdLibrary::getL ### ### Message: Can't find 1 Letter code for CA1 ### ### ### ### ### ### ### ### ### MTK++ Warning ### ### Function: stdLibrary::getL ### ### Message: Can't find 1 Letter code for CA1 ### ### ### ### ### ### ### ### ### MTK++ Warning ### ### Function: stdLibrary::getL ### ### Message: Can't find 1 Letter code for CA1 ### ### ### ### ### ### ### ### ### MTK++ Warning ### ### Function: stdLibrary::getL ### ### Message: Can't find 1 Letter code for CA1 ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: collection::determineMetalEnvironments ### ### Message: Metal Environments: GROUP:Zn-[DHHNX][] geom1 = tbp geom1RMSD = 10.9554 GROUP:Zn-[DDHXXX][] geom1 = oct geom1RMSD = 10.9778 ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: collection::assignMetalPartners ### ### Message: Number of Metal Groups = 1 ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: collection::assignMetalParameters ### ### Message: Metal Center: 1 Adding Primary Bonds: ZN@|ZN |-ASP96 @| OD2| dist = 2.33124 ZN@|ZN |-ASN128 @| OD1| dist = 2.05871 ZN@|ZN |-HID177 @| NE2| dist = 2.03857 ZN@|ZN |-HIE252 @| ND1| dist = 2.18854 ZN@|ZN |-CA1318 @|O3 | dist = 2.00938 ASP@| OD2|- ZN@|ZN |-ASN@| OD1| angle = 91.9471 ASP@| OD2|- ZN@|ZN |-HID@| NE2| angle = 86.7396 ASP@| OD2|- ZN@|ZN |-HIE@| ND1| angle = 168.904 ASP@| OD2|- ZN@|ZN |-CA1@|O3 | angle = 79.2622 ZN@| OD2|-ASP@| OD2|-ASP@| CG | angle = 124.976 ASN@| OD1|- ZN@|ZN |-HID@| NE2| angle = 87.4025 ASN@| OD1|- ZN@|ZN |-HIE@| ND1| angle = 99.1296 ASN@| OD1|- ZN@|ZN |-CA1@|O3 | angle = 138.692 ZN@| OD1|-ASN@| OD1|-ASN@| CG | angle = 136.791 HID@| NE2|- ZN@|ZN |-HIE@| ND1| angle = 94.3734 HID@| NE2|- ZN@|ZN |-CA1@|O3 | angle = 131.535 ZN@| NE2|-HID@| NE2|-HID@| CD2| angle = 127.264 ZN@| NE2|-HID@| NE2|-HID@| CE1| angle = 123.837 HIE@| ND1|- ZN@|ZN |-CA1@|O3 | angle = 91.8541 ZN@| ND1|-HIE@| ND1|-HIE@| CG | angle = 134.097 ZN@| ND1|-HIE@| ND1|-HIE@| CE1| angle = 116.308 ZN@|O3 |-CA1@|O3 |-CA1@|C9 | angle = 129.298 Metal Center: 2 Adding Primary Bonds: ZN@|ZN |-ASP67 @| OD2| dist = 2.10591 ZN@|ZN |-HID69 @| NE2| dist = 2.09378 ZN@|ZN |-ASP96 @| OD2| dist = 2.08563 ZN@|ZN |-CA1318 @|O3 | dist = 2.26925 ZN@|ZN |-CA1318 @|O2 | dist = 2.18159 ZN@|ZN |-CA1318 @|O1 | dist = 2.20311 ASP@| OD2|- ZN@|ZN |-HID@| NE2| angle = 107.363 ASP@| OD2|- ZN@|ZN |-ASP@| OD2| angle = 86.9797 ASP@| OD2|- ZN@|ZN |-CA1@|O3 | angle = 93.3837 ASP@| OD2|- ZN@|ZN |-CA1@|O2 | angle = 167.34 ASP@| OD2|- ZN@|ZN |-CA1@|O1 | angle = 92.1017 ZN@| OD2|-ASP@| OD2|-ASP@| CG | angle = 155.643 HID@| NE2|- ZN@|ZN |-ASP@| OD2| angle = 104.483 HID@| NE2|- ZN@|ZN |-CA1@|O3 | angle = 159.01 HID@| NE2|- ZN@|ZN |-CA1@|O2 | angle = 84.8121 HID@| NE2|- ZN@|ZN |-CA1@|O1 | angle = 89.9536 ZN@| NE2|-HID@| NE2|-HID@| CD2| angle = 128.876 ZN@| NE2|-HID@| NE2|-HID@| CE1| angle = 120.701 ASP@| OD2|- ZN@|ZN |-CA1@|O2 | angle = 93.403 ASP@| OD2|- ZN@|ZN |-CA1@|O1 | angle = 165.143 ZN@| OD2|-ASP@| OD2|-ASP@| CG | angle = 134.289 ZN@| OD2|-ASP@| OD2|- ZN@|ZN | angle = 98.1068 CA1@|O3 |- ZN@|ZN |-CA1@|O2 | angle = 74.295 CA1@|O3 |- ZN@|ZN |-CA1@|O1 | angle = 86.0511 ZN@|O3 |-CA1@|O3 |-CA1@|C9 | angle = 95.5147 CA1@|O2 |- ZN@|ZN |-CA1@|O1 | angle = 84.2871 ZN@|O2 |-CA1@|O2 |-CA1@|C8 | angle = 131.523 ZN@|O1 |-CA1@|O1 |-CA1@|C6 | angle = 109.338 ZN@|O1 |-CA1@|O1 |-CA1@|C2 | angle = 118.834 number of metal atoms = 2 number of metal centers = 2 number of metal groups = 1 ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: collection::assignMetalParameters ### ### Message: 3H68_OH is a match with rmsd of 5.1491 ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: writeLeap ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: writePdb ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: quit ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: MCPB Exited Normally ### ### ### ###