(base) ttgmod@LeCroissantNatur:~$ pdbfixer 3POV_finalmodelclean.pdb --add-atoms=heavy --keep-heterogens=all --output=3POV_fixed.pdb Command 'pdbfixer' not found, but can be installed with: sudo apt install python3-pdbfixer (base) ttgmod@LeCroissantNatur:~$ cd ~/"3POV for MD sim" (base) ttgmod@LeCroissantNatur:~/3POV for MD sim$ conda activate md_sim (md_sim) ttgmod@LeCroissantNatur:~/3POV for MD sim$ pdbfixer 3POV_finalmodelclean.pdb --add-atoms=heavy --keep-heterogens=all --output=3POV_fixed.pdb (md_sim) ttgmod@LeCroissantNatur:~/3POV for MD sim$ reduce -build -nuclear 3POV_fixed.pdb > 3POV_reduced.pdb Processing file: "3POV_fixed.pdb" Building His ring NH Hydrogens. Building or keeping OH & SH Hydrogens. Rotating existing OH & SH Hydrogens SKIPPED H( A 56 GLNHE21 ): A 56 GLN NE2 bonds- A 472 LYS CE (H bumps) SKIPPED H( A 56 GLNHE22 ): A 56 GLN NE2 bonds- A 472 LYS CE (H bumps) WARNING: A 472 LYS NZ H atom too close to A 56 GLN NE2 by -0.503248A if warning inappropriate, adjust the cuttoffs using -METALBump or -NONMETALBump. WARNING: A 472 LYS NZ H atom too close to A 472 LYS CE by -0.231558A if warning inappropriate, adjust the cuttoffs using -METALBump or -NONMETALBump. WARNING: A 472 LYS NZ H atom too close to A 56 GLN NE2 by -0.838411A if warning inappropriate, adjust the cuttoffs using -METALBump or -NONMETALBump. WARNING: A 472 LYS NZ H atom too close to A 472 LYS CE by -0.231558A if warning inappropriate, adjust the cuttoffs using -METALBump or -NONMETALBump. WARNING: A 472 LYS NZ H atom too close to A 472 LYS CE by -0.231558A if warning inappropriate, adjust the cuttoffs using -METALBump or -NONMETALBump. SKIPPED H( A 472 LYS HZ3 ): A 472 LYS NZ bonds- A 56 GLN NE2 (NH2R) SKIPPED H( A 485 SER H ): A 485 SER N bonds- A 484 HIS CB (H bumps) VDW dot density = 16/A^2 Probe radius = 0.25A Orientation penalty scale = 1 (100%) Eliminate contacts within 3 bonds. Ignore atoms with |occupancy| <= 0.01 during adjustments. Waters ignored if B-Factor >= 40 or |occupancy| < 0.66 Aromatic rings in amino acids accept hydrogen bonds. Flipping Asn, Gln and His groups. For each flip state, bumps where gap is more than 0.4A are indicated with '!'. Rotating NH3 Hydrogens. Not processing Met methyls. Singles(size 130): A 4 THR OG1 : A 6 THR OG1 : A -1 GLY N : A 15 TYR OH : A 19 THR OG1 : A 24 THR OG1 : A 28 GLN : A 29 GLN : A 34 SER OG : A 36 SER OG : A 38 SER OG : A 39 LYS NZ : A 42 LYS NZ : A 43 HIS : A 45 LYS NZ : A 50 CYS SG : A 52 GLN : A 54 LYS NZ : A 66 TYR OH : A 68 TYR OH : A 72 SER OG : A 80 SER OG : A 84 CYS SG : A 85 ASN : A 102 SER OG : A 107 CYS SG : A 108 SER OG : A 109 GLN : A 111 ASN : A 113 HIS : A 114 GLN : A 117 HIS : A 119 CYS SG : A 126 THR OG1 : A 127 SER OG : A 128 SER OG : A 129 GLN : A 130 SER OG : A 132 ASN : A 147 LYS NZ : A 154 GLN : A 155 GLN : A 156 ASN : A 157 THR OG1 : A 158 SER OG : A 159 LYS NZ : A 160 LYS NZ : A 163 SER OG : A 168 THR OG1 : A 169 ASN : A 170 ASN : A 171 HIS : A 183 CYS SG : A 188 LYS NZ : A 189 THR OG1 : A 193 THR OG1 : A 200 THR OG1 : A 201 ASN : A 205 TYR OH : A 212 GLN : A 219 SER OG : A 225 ASN : A 227 LYS NZ : A 228 THR OG1 : A 230 THR OG1 : A 239 ASN : A 240 CYS SG : A 241 LYS NZ : A 247 CYS SG : A 250 LYS NZ : A 251 TYR OH : A 252 THR OG1 : A 258 CYS SG : A 265 TYR OH : A 269 TYR OH : A 274 LYS NZ : A 278 LYS NZ : A 282 TYR OH : A 283 SER OG : A 285 SER OG : A 286 LYS NZ : A 291 TYR OH : A 296 LYS NZ : A 307 TYR OH : A 309 GLN : A 314 CYS SG : A 317 LYS NZ : A 318 LYS NZ : A 320 LYS NZ : A 326 ASN : A 331 CYS SG : A 334 HIS : A 335 ASN : A 336 SER OG : A 337 THR OG1 : A 343 TYR OH : A 354 GLN : A 358 LYS NZ : A 362 LYS NZ : A 364 ASN : A 368 ASN : A 371 HIS : A 373 TYR OH : A 375 TYR OH : A 387 TYR OH : A 392 SER OG : A 399 SER OG : A 401 LYS NZ : A 402 TYR OH : A 403 TYR OH : A 411 LYS NZ : A 414 TYR OH : A 415 GLN : A 419 ASN : A 420 CYS SG : A 421 THR OG1 : A 430 HIS : A 435 THR OG1 : A 450 HIS : A 454 HIS : A 455 GLN : A 458 ASN : A 461 SER OG : A 463 SER OG : A 465 LYS NZ : A 467 THR OG1 : A 470 TYR OH : A 472 LYS NZ : A 476 SER OG : A 479 SER OG Set 1 (size 5): A 484 HIS : A 481 ASN : A 477 TYR OH : A 213 ASN : A 210 SER OG Set 2 (size 2): A 303 TYR OH : A 406 THR OG1 Set 3 (size 2): A 485 SER OG : A 382 SER OG Set 4 (size 2): A 449 LYS NZ : A 381 SER OG Set 5 (size 3): A 346 THR OG1 : A 356 SER OG : A 351 THR OG1 Set 6 (size 2): A 340 SER OG : A 440 THR OG1 Set 7 (size 2): A 338 THR OG1 : A 443 TYR OH Set 8 (size 2): A 325 HIS : A 322 THR OG1 Set 9 (size 2): A 301 SER OG : A 299 SER OG Set 10 (size 2): A 266 GLN : A 262 TYR OH Set 11 (size 2): A 255 LYS NZ : A 349 GLN Set 12 (size 2): A 246 LYS NZ : A 376 GLN Set 13 (size 2): A 202 CYS SG : A 235 GLN Set 14 (size 2): A 196 HIS : A 243 TYR OH Set 15 (size 3): A 149 HIS : A 153 LYS NZ : A 372 SER OG Set 16 (size 2): A 380 GLN : A 145 SER OG Set 17 (size 2): A 146 SER OG : A 144 SER OG Set 18 (size 2): A 116 HIS : A 120 CYS SG Set 19 (size 2): A 12 SER OG : A 73 LYS NZ Set 20 (size 2): A 67 ASN : A 209 GLN Set 21 (size 2): A 58 SER OG : A 104 TYR OH orientation 4: A 4 THR OG1 : rot 178: bump=-0.023, HB=1.272, total=2.361 orientation 1: A 6 THR OG1 : rot -171: bump=-0.058, HB=0.000, total=0.710 orientation 3: A -1 GLY N :NH3+ 151: bump=0.000, HB=0.076, total=0.479 orientation 1: A 15 TYR OH : rot 179: bump=0.000, HB=0.000, total=0.041 orientation 2: A 19 THR OG1 : rot -36: bump=0.000, HB=0.958, total=1.615 orientation 1: A 24 THR OG1 : rot -172: bump=-0.791, HB=0.223, total=0.463, BADBUMP orientation 1: A 28 GLN : amide: bump=-0.054, HB=0.005, total=1.935 orientation 1: A 29 GLN : amide: bump=0.000, HB=0.000, total=0.739 orientation 4: A 34 SER OG : rot -128: bump=-0.452, HB=0.051, total=2.569 orientation 3: A 36 SER OG : rot 109: bump=0.000, HB=1.237, total=2.369 orientation 4: A 38 SER OG : rot 74: bump=-0.991, HB=1.082, total=2.874 orientation 2: A 39 LYS NZ :NH3+ -148: bump=0.000, HB=0.000, total=0.122 orientation 3: A 42 LYS NZ :NH3+ 145: bump=0.000, HB=0.000, total=0.158 orientation 1: A 43 HIS : no HD1: bump=-1.569, HB=0.676, total=7.806 orientation 3: A 45 LYS NZ :NH3+ 134: bump=-1.330, HB=0.000, total=0.489 orientation 1: A 50 CYS SG : rot 147: bump=-0.479, HB=0.000, total=2.090 orientation 2: A 52 GLN :FLIP amide: bump=-1.587, HB=0.000, total=-0.964 orientation 2: A 54 LYS NZ :NH3+ -155: bump=0.000, HB=0.000, total=0.160 orientation 10: A 66 TYR OH : rot -132: bump=-0.316, HB=0.000, total=2.039 orientation 12: A 68 TYR OH : rot -156: bump=0.000, HB=0.000, total=1.006 orientation 2: A 72 SER OG : rot -32: bump=0.000, HB=0.000, total=0.495 orientation 1: A 80 SER OG : rot 141: bump=-0.169, HB=0.000, total=3.095 orientation 4: A 84 CYS SG : rot -64: bump=-1.460, HB=0.009, total=2.586 orientation 2: A 85 ASN :FLIP amide: bump=-4.200, HB=0.000, total=-1.846, BADBUMP orientation 2: A 102 SER OG : rot -37: bump=-0.497, HB=0.000, total=0.513 orientation 1: A 107 CYS SG : rot 110: bump=-0.113, HB=0.000, total=3.777 orientation 2: A 108 SER OG : rot 1: bump=-0.041, HB=1.128, total=2.682 orientation 1: A 109 GLN : amide: bump=0.000, HB=0.000, total=0.313 orientation 1: A 111 ASN : amide: bump=-0.731, HB=0.386, total=3.033 orientation 4: A 113 HIS :FLIP no HD1: bump=-0.010, HB=0.000, total=1.292 orientation 1: A 114 GLN : amide: bump=-0.035, HB=0.026, total=2.142 orientation 1: A 117 HIS : no HD1: bump=-3.667, HB=0.000, total=0.263, BADBUMP orientation 2: A 119 CYS SG : rot -164: bump=-0.991, HB=0.000, total=3.233 orientation 2: A 126 THR OG1 : rot -1: bump=-0.057, HB=0.803, total=4.215 orientation 2: A 127 SER OG : rot 61: bump=-0.059, HB=0.000, total=0.412 orientation 1: A 128 SER OG : rot 180: bump=-2.088, HB=0.000, total=-1.844, BADBUMP orientation 2: A 129 GLN :FLIP amide: bump=0.000, HB=0.000, total=0.421 orientation 2: A 130 SER OG : rot -13: bump=-0.327, HB=0.029, total=0.330 orientation 1: A 132 ASN : amide: bump=-6.085, HB=0.000, total=-3.741, BADBUMP orientation 3: A 147 LYS NZ :NH3+ 139: bump=-0.104, HB=0.000, total=1.416 orientation 1: A 154 GLN : amide: bump=-2.105, HB=0.000, total=0.233, BADBUMP orientation 1: A 155 GLN : amide: bump=-0.489, HB=0.024, total=1.942 orientation 2: A 156 ASN :FLIP amide: bump=0.000, HB=0.000, total=1.726 orientation 7: A 157 THR OG1 : rot -23: bump=-0.592, HB=1.150, total=1.915 orientation 4: A 158 SER OG : rot -2: bump=-0.421, HB=1.093, total=0.981, BADBUMP orientation 3: A 159 LYS NZ :NH3+ 159: bump=-0.020, HB=0.000, total=0.402 orientation 3: A 160 LYS NZ :NH3+ 142: bump=-0.793, HB=1.233, total=3.014 orientation 1: A 163 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 168 THR OG1 : rot -170: bump=-0.054, HB=0.000, total=0.323 orientation 1: A 169 ASN : amide: bump=-0.400, HB=0.943, total=1.829 orientation 2: A 170 ASN :FLIP amide: bump=-0.019, HB=0.144, total=0.867 orientation 1: A 171 HIS : no HD1: bump=0.000, HB=0.000, total=0.000 orientation 3: A 183 CYS SG : rot 56: bump=-0.013, HB=0.000, total=3.627 orientation 3: A 188 LYS NZ :NH3+ 148: bump=0.000, HB=0.225, total=2.148 orientation 2: A 189 THR OG1 : rot 73: bump=0.000, HB=0.250, total=1.025 orientation 1: A 193 THR OG1 : rot 171: bump=0.000, HB=0.000, total=1.379 orientation 1: A 200 THR OG1 : rot 171: bump=-0.012, HB=0.000, total=1.868 orientation 1: A 201 ASN : amide: bump=-0.354, HB=0.332, total=2.515 orientation 10: A 205 TYR OH : rot -83: bump=-1.148, HB=0.000, total=0.302 orientation 2: A 212 GLN :FLIP amide: bump=-0.297, HB=0.286, total=1.499 orientation 2: A 219 SER OG : rot 126: bump=0.000, HB=0.003, total=2.769 orientation 1: A 225 ASN : amide: bump=0.000, HB=0.000, total=1.023 orientation 3: A 227 LYS NZ :NH3+ 147: bump=0.000, HB=0.000, total=0.125 orientation 1: A 228 THR OG1 : rot -171: bump=0.000, HB=0.000, total=0.125 orientation 4: A 230 THR OG1 : rot 34: bump=-0.035, HB=1.081, total=1.288 orientation 1: A 239 ASN : amide: bump=0.000, HB=0.000, total=0.620 orientation 2: A 240 CYS SG : rot 28: bump=-0.297, HB=0.004, total=3.647 orientation 2: A 241 LYS NZ :NH3+ -142: bump=0.000, HB=0.000, total=0.136 orientation 1: A 247 CYS SG : rot 141: bump=0.000, HB=0.000, total=3.670 orientation 3: A 250 LYS NZ :NH3+ 139: bump=-0.013, HB=1.664, total=2.690 orientation 8: A 251 TYR OH : rot -24: bump=-1.249, HB=1.561, total=2.159 orientation 1: A 252 THR OG1 : rot -134: bump=-0.248, HB=0.666, total=2.340 orientation 1: A 258 CYS SG : rot 180: bump=-1.250, HB=0.003, total=0.070 orientation 9: A 265 TYR OH : rot -71: bump=0.000, HB=0.252, total=0.953 orientation 9: A 269 TYR OH : rot -120: bump=0.000, HB=0.090, total=1.610 orientation 2: A 274 LYS NZ :NH3+ -154: bump=-0.140, HB=1.294, total=2.129 orientation 4: A 278 LYS NZ :NH3+ -145: bump=0.000, HB=1.564, total=2.617 orientation 1: A 282 TYR OH : rot -170: bump=-0.009, HB=1.238, total=1.256 orientation 2: A 283 SER OG : rot -58: bump=-0.111, HB=1.050, total=2.818 orientation 1: A 285 SER OG : rot 180: bump=0.000, HB=0.000, total=0.459 orientation 2: A 286 LYS NZ :NH3+ -145: bump=0.000, HB=0.000, total=0.125 orientation 5: A 291 TYR OH : rot 15: bump=-0.010, HB=0.000, total=1.439 orientation 4: A 296 LYS NZ :NH3+ -128: bump=0.000, HB=0.000, total=0.801 orientation 9: A 307 TYR OH : rot -141: bump=-0.131, HB=0.000, total=2.636 orientation 2: A 309 GLN :FLIP amide: bump=0.000, HB=0.005, total=1.744 orientation 3: A 314 CYS SG : rot -8: bump=-0.028, HB=0.778, total=0.869 orientation 2: A 317 LYS NZ :NH3+ -153: bump=0.000, HB=0.000, total=0.163 orientation 4: A 318 LYS NZ :NH3+ -139: bump=-3.181, HB=0.132, total=-1.587, BADBUMP orientation 2: A 320 LYS NZ :NH3+ -156: bump=0.000, HB=0.000, total=0.156 orientation 1: A 326 ASN : amide: bump=-0.001, HB=0.000, total=0.558 orientation 3: A 331 CYS SG : rot -123: bump=-0.075, HB=0.000, total=1.824 orientation 2: A 334 HIS : no HE2: bump=-0.142, HB=0.538, total=3.061 orientation 1: A 335 ASN : amide: bump=0.000, HB=2.070, total=4.822 orientation 2: A 336 SER OG : rot 52: bump=0.000, HB=0.000, total=0.981 orientation 2: A 337 THR OG1 : rot -1: bump=0.000, HB=0.000, total=1.050 orientation 4: A 343 TYR OH : rot 130: bump=-0.268, HB=0.000, total=1.375 orientation 2: A 354 GLN :FLIP amide: bump=0.000, HB=0.000, total=0.386 orientation 1: A 358 LYS NZ :NH3+ -175: bump=-0.150, HB=0.000, total=1.556 orientation 3: A 362 LYS NZ :NH3+ 152: bump=-0.435, HB=1.513, total=1.606 orientation 1: A 364 ASN : amide: bump=-1.354, HB=1.956, total=4.605 orientation 1: A 368 ASN : amide: bump=-0.219, HB=2.041, total=4.656 orientation 1: A 371 HIS : no HD1: bump=-1.490, HB=0.923, total=8.024 orientation 10: A 373 TYR OH : rot -155: bump=-1.424, HB=0.405, total=0.071 orientation 1: A 375 TYR OH : rot 173: bump=0.000, HB=0.000, total=0.052 orientation 7: A 387 TYR OH : rot 4: bump=-1.908, HB=1.172, total=0.651, BADBUMP orientation 8: A 392 SER OG : rot -68: bump=-1.839, HB=1.771, total=2.573 orientation 2: A 399 SER OG : rot -16: bump=-0.408, HB=0.291, total=2.490 orientation 3: A 401 LYS NZ :NH3+ 152: bump=0.000, HB=0.000, total=0.159 orientation 3: A 402 TYR OH : rot 146: bump=-1.176, HB=0.000, total=1.415 orientation 8: A 403 TYR OH : rot -5: bump=-0.259, HB=0.000, total=1.781 orientation 3: A 411 LYS NZ :NH3+ 130: bump=-0.022, HB=0.000, total=1.947 orientation 1: A 414 TYR OH : rot -176: bump=0.000, HB=0.000, total=0.037 orientation 1: A 415 GLN : amide: bump=0.000, HB=0.000, total=0.451 orientation 1: A 419 ASN : amide: bump=0.000, HB=0.000, total=0.852 orientation 2: A 420 CYS SG : rot 56: bump=0.000, HB=0.048, total=2.013 orientation 1: A 421 THR OG1 : rot -171: bump=-0.005, HB=0.000, total=1.272 orientation 2: A 430 HIS : no HE2: bump=-0.022, HB=0.010, total=2.154 orientation 2: A 435 THR OG1 : rot -40: bump=-0.135, HB=0.089, total=2.050 orientation 2: A 450 HIS : no HE2: bump=-1.760, HB=0.948, total=2.221 orientation 1: A 454 HIS : no HD1: bump=0.000, HB=0.000, total=0.989 orientation 2: A 455 GLN :FLIP amide: bump=-4.416, HB=0.000, total=-0.647, BADBUMP orientation 2: A 458 ASN :FLIP amide: bump=-0.135, HB=0.000, total=0.330 orientation 2: A 461 SER OG : rot 67: bump=0.000, HB=0.168, total=1.191 orientation 5: A 463 SER OG : rot 60: bump=-0.053, HB=1.288, total=1.719 orientation 3: A 465 LYS NZ :NH3+ 156: bump=0.000, HB=0.000, total=0.146 orientation 1: A 467 THR OG1 : rot 171: bump=0.000, HB=0.000, total=1.070 orientation 4: A 470 TYR OH : rot 117: bump=-1.473, HB=0.017, total=2.122 orientation 2: A 472 LYS NZ :NH3+ -145: bump=0.000, HB=0.000, total=0.181 orientation 2: A 476 SER OG : rot 83: bump=0.000, HB=0.912, total=1.631 orientation 2: A 479 SER OG : rot -14: bump=-0.188, HB=0.117, total=1.132 Processing set: A 484 HIS [6]: A 481 ASN [2]: A 477 TYR OH [11] : A 213 ASN [2]: A 210 SER OG [5] permutations: 1320 Computing dot scores Num optimizations problems to be solved for this clique: 7 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: -66.132 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : -66.298 Optimal score following high resolution, local optimization: -66.298 Processing set: A 303 TYR OH [12]: A 406 THR OG1 [3] permutations: 36 Computing dot scores Num optimizations problems to be solved for this clique: 1 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 4.880 > : 5.253 Optimal score following high resolution, local optimization: 5.253 Processing set: A 485 SER OG [5]: A 382 SER OG [3] permutations: 15 Computing dot scores Num optimizations problems to be solved for this clique: 1 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: -3.250 > : -3.212 Optimal score following high resolution, local optimization: -3.212 Processing set: A 449 LYS NZ [4]: A 381 SER OG [7] permutations: 28 Computing dot scores Num optimizations problems to be solved for this clique: 1 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 6.733 > : 6.962 Optimal score following high resolution, local optimization: 6.962 Processing set: A 346 THR OG1 [3]: A 356 SER OG [1]: A 351 THR OG1 [7] permutations: 21 Computing dot scores Num optimizations problems to be solved for this clique: 1 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 5.031 > : 5.021 Optimal score following high resolution, local optimization: 5.021 Processing set: A 340 SER OG [3]: A 440 THR OG1 [2] permutations: 6 Computing dot scores Num optimizations problems to be solved for this clique: 1 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 4.940 > : 5.414 Optimal score following high resolution, local optimization: 5.414 Processing set: A 338 THR OG1 [4]: A 443 TYR OH [12] permutations: 48 Computing dot scores Num optimizations problems to be solved for this clique: 1 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 3.983 > : 4.205 Optimal score following high resolution, local optimization: 4.205 Processing set: A 325 HIS [6]: A 322 THR OG1 [4] permutations: 24 Computing dot scores Num optimizations problems to be solved for this clique: 5 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 5.644 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : 6.373 Optimal score following high resolution, local optimization: 6.373 Processing set: A 301 SER OG [2]: A 299 SER OG [5] permutations: 10 Computing dot scores Num optimizations problems to be solved for this clique: 1 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 4.271 > : 4.544 Optimal score following high resolution, local optimization: 4.544 Processing set: A 266 GLN [2]: A 262 TYR OH [12] permutations: 24 Computing dot scores Num optimizations problems to be solved for this clique: 3 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 2.760 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : 3.762 Optimal score following high resolution, local optimization: 3.762 Processing set: A 255 LYS NZ [4]: A 349 GLN [2] permutations: 8 Computing dot scores Num optimizations problems to be solved for this clique: 3 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 3.555 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : 3.199 Optimal score following high resolution, local optimization: 3.199 Processing set: A 246 LYS NZ [4]: A 376 GLN [2] permutations: 8 Computing dot scores Num optimizations problems to be solved for this clique: 3 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 3.873 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : 4.018 Optimal score following high resolution, local optimization: 4.018 Processing set: A 202 CYS SG [5]: A 235 GLN [2] permutations: 10 Computing dot scores Num optimizations problems to be solved for this clique: 3 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 4.372 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : 4.514 Optimal score following high resolution, local optimization: 4.514 Processing set: A 196 HIS [6]: A 243 TYR OH [14] permutations: 84 Computing dot scores Num optimizations problems to be solved for this clique: 5 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 8.742 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : 8.720 Optimal score following high resolution, local optimization: 8.720 Processing set: A 149 HIS [6]: A 153 LYS NZ [4]: A 372 SER OG [2] permutations: 48 Computing dot scores Num optimizations problems to be solved for this clique: 5 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 6.592 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : 6.617 Optimal score following high resolution, local optimization: 6.617 Processing set: A 380 GLN [2]: A 145 SER OG [1] permutations: 2 Computing dot scores Num optimizations problems to be solved for this clique: 3 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 3.315 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : 4.305 Optimal score following high resolution, local optimization: 4.305 Processing set: A 146 SER OG [1]: A 144 SER OG [2] permutations: 2 Computing dot scores Num optimizations problems to be solved for this clique: 1 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: -9.288 > : -8.905 Optimal score following high resolution, local optimization: -8.905 Processing set: A 116 HIS [6]: A 120 CYS SG [4] permutations: 24 Computing dot scores Num optimizations problems to be solved for this clique: 5 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 5.483 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : 6.275 Optimal score following high resolution, local optimization: 6.275 Processing set: A 12 SER OG [4]: A 73 LYS NZ [4] permutations: 16 Computing dot scores Num optimizations problems to be solved for this clique: 1 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 6.633 > : 7.343 Optimal score following high resolution, local optimization: 7.343 Processing set: A 67 ASN [2]: A 209 GLN [2] permutations: 4 Computing dot scores Num optimizations problems to be solved for this clique: 4 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 6.077 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following high resolution, local optimization: 6.077 Processing set: A 58 SER OG [2]: A 104 TYR OH [11] permutations: 22 Computing dot scores Num optimizations problems to be solved for this clique: 1 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 1.526 > : 1.670 Optimal score following high resolution, local optimization: 1.670 Found 0 hydrogens (0 hets) Standardized 0 hydrogens (0 hets) Added 3836 hydrogens (0 hets) Adjusted 148 group(s) If you publish work which uses reduce, please cite: Word, et. al. (1999) J. Mol. Biol. 285, 1735-1747. For more information see http://kinemage.biochem.duke.edu (md_sim) ttgmod@LeCroissantNatur:~/3POV for MD sim$ pdb4amber -i 3POV_reduced.pdb -o 3POV_amber.pdb --dry ================================================== Summary of pdb4amber for: 3POV_reduced.pdb =================================================== ----------Chains The following (original) chains have been found: A ---------- Alternate Locations (Original Residues!)) The following residues had alternate locations: None -----------Non-standard-resnames ---------- Missing heavy atom(s) None (md_sim) ttgmod@LeCroissantNatur:~/3POV for MD sim$ tleap -I: Adding /home/ttgmod/miniconda3/envs/md_sim/dat/leap/prep to search path. -I: Adding /home/ttgmod/miniconda3/envs/md_sim/dat/leap/lib to search path. -I: Adding /home/ttgmod/miniconda3/envs/md_sim/dat/leap/parm to search path. -I: Adding /home/ttgmod/miniconda3/envs/md_sim/dat/leap/cmd to search path. Welcome to LEaP! (no leaprc in search path) > source leaprc.protein.ff14SB ----- Source: /home/ttgmod/miniconda3/envs/md_sim/dat/leap/cmd/leaprc.protein.ff14SB ----- Source of /home/ttgmod/miniconda3/envs/md_sim/dat/leap/cmd/leaprc.protein.ff14SB done Log file: ./leap.log Loading parameters: /home/ttgmod/miniconda3/envs/md_sim/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA Loading parameters: /home/ttgmod/miniconda3/envs/md_sim/dat/leap/parm/frcmod.ff14SB Reading force field modification type file (frcmod) Reading title: ff14SB protein backbone and sidechain parameters Loading library: /home/ttgmod/miniconda3/envs/md_sim/dat/leap/lib/amino12.lib Loading library: /home/ttgmod/miniconda3/envs/md_sim/dat/leap/lib/aminoct12.lib Loading library: /home/ttgmod/miniconda3/envs/md_sim/dat/leap/lib/aminont12.lib > source leaprc.water.tip3p ----- Source: /home/ttgmod/miniconda3/envs/md_sim/dat/leap/cmd/leaprc.water.tip3p ----- Source of /home/ttgmod/miniconda3/envs/md_sim/dat/leap/cmd/leaprc.water.tip3p done Loading library: /home/ttgmod/miniconda3/envs/md_sim/dat/leap/lib/atomic_ions.lib Loading library: /home/ttgmod/miniconda3/envs/md_sim/dat/leap/lib/solvents.lib Loading parameters: /home/ttgmod/miniconda3/envs/md_sim/dat/leap/parm/frcmod.tip3p Reading force field modification type file (frcmod) Reading title: This is the additional/replacement parameter set for TIP3P water Loading parameters: /home/ttgmod/miniconda3/envs/md_sim/dat/leap/parm/frcmod.ions1lm_126_tip3p Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of monovalent ions for TIP3P water model (12-6 normal usage set) Loading parameters: /home/ttgmod/miniconda3/envs/md_sim/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) Loading parameters: /home/ttgmod/miniconda3/envs/md_sim/dat/leap/parm/frcmod.ions234lm_126_tip3p Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of divalent to tetravalent ions for TIP3P water model (12-6 normal usage set) > mol = loadpdb 3POV_amber.pdb Loading PDB file: ./3POV_amber.pdb total atoms in file: 7727 Leap added 4 missing atoms according to residue templates: 4 H / lone pairs > check mol Checking 'mol'.... Warning: The unperturbed charge of the unit (8.000000) is not zero. Warning: Close contact of 1.497 angstroms between nonbonded atoms O and H ------- .R.A and .R.A Warning: Close contact of 1.328 angstroms between nonbonded atoms HD21 and HD11 ------- .R.A and .R.A Warning: Close contact of 1.490 angstroms between nonbonded atoms HD23 and H ------- .R.A and .R.A Warning: Close contact of 1.484 angstroms between nonbonded atoms HD22 and HB2 ------- .R.A and .R.A Warning: Close contact of 1.150 angstroms between nonbonded atoms HE22 and CE ------- .R.A and .R.A Warning: Close contact of 1.194 angstroms between nonbonded atoms HE22 and HD3 ------- .R.A and .R.A Warning: Close contact of 1.168 angstroms between nonbonded atoms HE22 and CD ------- .R.A and .R.A Warning: Close contact of 1.287 angstroms between nonbonded atoms HE21 and HZ3 ------- .R.A and .R.A Warning: Close contact of 1.378 angstroms between nonbonded atoms HE21 and NZ ------- .R.A and .R.A Warning: Close contact of 1.084 angstroms between nonbonded atoms HE21 and HE2 ------- .R.A and .R.A Warning: Close contact of 1.336 angstroms between nonbonded atoms HE21 and CE ------- .R.A and .R.A Warning: Close contact of 1.475 angstroms between nonbonded atoms NE2 and HZ3 ------- .R.A and .R.A Warning: Close contact of 1.041 angstroms between nonbonded atoms NE2 and HE2 ------- .R.A and .R.A Warning: Close contact of 1.240 angstroms between nonbonded atoms NE2 and CE ------- .R.A and .R.A Warning: Close contact of 1.471 angstroms between nonbonded atoms HG2 and HD3 ------- .R.A and .R.A Warning: Close contact of 1.392 angstroms between nonbonded atoms HE2 and HG3 ------- .R.A and .R.A Warning: Close contact of 1.498 angstroms between nonbonded atoms HD2 and HD11 ------- .R.A and .R.A Warning: Close contact of 1.453 angstroms between nonbonded atoms HH21 and HE22 ------- .R.A and .R.A Warning: Close contact of 1.203 angstroms between nonbonded atoms HG2 and H ------- .R.A and .R.A Warning: Close contact of 1.138 angstroms between nonbonded atoms HH22 and HG ------- .R.A and .R.A Warning: Close contact of 1.121 angstroms between nonbonded atoms HH22 and OG ------- .R.A and .R.A Warning: Close contact of 1.122 angstroms between nonbonded atoms HB3 and H ------- .R.A and .R.A Warning: Close contact of 1.129 angstroms between nonbonded atoms HZ and HG3 ------- .R.A and .R.A Warning: Close contact of 1.439 angstroms between nonbonded atoms HD1 and HH21 ------- .R.A and .R.A Warning: Close contact of 1.237 angstroms between nonbonded atoms HE1 and HG ------- .R.A and .R.A Warning: Close contact of 1.078 angstroms between nonbonded atoms HB2 and HB2 ------- .R.A and .R.A Warning: Close contact of 1.272 angstroms between nonbonded atoms HB3 and HD21 ------- .R.A and .R.A Warning: Close contact of 0.946 angstroms between nonbonded atoms HD22 and H ------- .R.A and .R.A Warning: Close contact of 1.163 angstroms between nonbonded atoms HG13 and HD3 ------- .R.A and .R.A Warning: Close contact of 0.959 angstroms between nonbonded atoms HG11 and HB3 ------- .R.A and .R.A Warning: Close contact of 1.307 angstroms between nonbonded atoms HG11 and CB ------- .R.A and .R.A Warning: Close contact of 1.248 angstroms between nonbonded atoms HG11 and HG3 ------- .R.A and .R.A Warning: Close contact of 1.492 angstroms between nonbonded atoms HG11 and CG ------- .R.A and .R.A Warning: Close contact of 1.326 angstroms between nonbonded atoms HD22 and C ------- .R.A and .R.A Warning: Close contact of 1.290 angstroms between nonbonded atoms HD22 and HD2 ------- .R.A and .R.A Warning: Close contact of 1.416 angstroms between nonbonded atoms HD22 and CD ------- .R.A and .R.A Warning: Close contact of 1.463 angstroms between nonbonded atoms HD22 and N ------- .R.A and .R.A Warning: Close contact of 1.347 angstroms between nonbonded atoms HD21 and HA ------- .R.A and .R.A Warning: Close contact of 1.269 angstroms between nonbonded atoms HB3 and HG2 ------- .R.A and .R.A Warning: Close contact of 1.211 angstroms between nonbonded atoms HA and HB2 ------- .R.A and .R.A Warning: Close contact of 1.034 angstroms between nonbonded atoms HD12 and HA ------- .R.A and .R.A Warning: Close contact of 1.324 angstroms between nonbonded atoms HD12 and HD3 ------- .R.A and .R.A Warning: Close contact of 1.352 angstroms between nonbonded atoms HG12 and CG ------- .R.A and .R.A Warning: Close contact of 1.231 angstroms between nonbonded atoms HB and OXT ------- .R.A and .R.A Warning: Close contact of 1.403 angstroms between nonbonded atoms HB and C ------- .R.A and .R.A Warning: Close contact of 1.155 angstroms between nonbonded atoms HE1 and HE1 ------- .R.A and .R.A Warning: Close contact of 1.327 angstroms between nonbonded atoms HD1 and HE2 ------- .R.A and .R.A Warning: Close contact of 1.391 angstroms between nonbonded atoms HB and HD2 ------- .R.A and .R.A Warning: Close contact of 0.414 angstroms between nonbonded atoms HB3 and H ------- .R.A and .R.A Warning: Close contact of 0.993 angstroms between nonbonded atoms HB3 and N ------- .R.A and .R.A Warning: Close contact of 1.442 angstroms between nonbonded atoms HB2 and H ------- .R.A and .R.A Warning: Close contact of 1.044 angstroms between nonbonded atoms CB and H ------- .R.A and .R.A Warning: Close contact of 0.980 angstroms between nonbonded atoms O and HD2 ------- .R.A and .R.A Warning: Close contact of 1.471 angstroms between nonbonded atoms O and CD ------- .R.A and .R.A Checking parameters for unit 'mol'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 55 Unit is OK. >