***************************************************** * AMBER Bond Angle and Dihedral Parameter Optimiser * * * * v3.0.0 * * * * Written by: * * Robin Betz (2011) * * Ross Walker (2004) * * The Walker Molecular Dynamics Lab * * University of California, San Diego * * La Jolla, California, 92092 * * USA * ***************************************************** ************************************************************************************* Execution started at: | Mon Jun 16 15:44:15 2014 | | Random seed = 1402958655 Reading job control file: job_multi_fit.in Job Control: Read a total of 19 lines from job_control file. 18 options set. Reading prmtop file list: prmtops_list Reading prmtop file : a.prmtop Reading prmtop file : b.prmtop Reading prmtop file : c.prmtop Prmtop (info): Successfully read in saved parameter information Prmtop (unique): Found 8 unique bonds. Prmtop (unique): Found 16 unique angles. Prmtop (unique): Found 23 unique dihedrals. Prmtop (unique): Found 38 unique dihedral terms. Prmtop (info): Successfully read in saved parameter information Prmtop (unique): Found 7 unique bonds. Prmtop (unique): Found 12 unique angles. Prmtop (unique): Found 16 unique dihedrals. Prmtop (unique): Found 27 unique dihedral terms. Prmtop (info): Successfully read in saved parameter information Prmtop (unique): Found 8 unique bonds. Prmtop (unique): Found 16 unique angles. Prmtop (unique): Found 23 unique dihedrals. Prmtop (unique): Found 38 unique dihedral terms. Reading mdcrd file list: mdcrds_list Reading mdcrd file : A_valid_structures.mdcrd Coordinate file passed format check Reading mdcrd file : B_valid_structures.mdcrd Coordinate file passed format check Reading mdcrd file : C_valid_structures.mdcrd Coordinate file passed format check Reading energy file or directory : quantum_A_weighted.dat Structure 6 weight = 0.000000 Structure 16 weight = 0.000000 Reading energy file or directory : quantum_B.dat Reading energy file or directory : quantum_C_weighted.dat Structure 8 weight = 0.000000 --------------------------------------------------------------------- | OPTIONS SUMMARY | | --------------- | | Summary of Run Type Options: | | Run Mode = FIT, Minimiser = GENETIC | | Function to be Fit = SUM_SQUARES_AMBER_STANDARD | | | | Terms to be fit: | | UNIQUE_BONDS = 8, UNIQUE ANGLES = 16, UNIQUE DIHEDRALS = 23 | | NBONDS = 31, NANGLES = 54, NDIHEDRALS = 105 | | Total dimensions of fit = 8 | | | | Sample structures for least squares fit = 60 | | | | | | Energy Correction Term (K) = -466382.13570900 | | | | OPTIMIZATIONS = 50 | | MAX GENERATIONS = 10000 | | MUTATION RATE = 0.10 | | | | Estimate Memory Usage (per cpu): | | Coordinate info will be read from disk as required. | | OPTION STORAGE = 74 bytes | | PRMTOP STORAGE = 1363750 bytes | | COORDINATE STORAGE = 45720 bytes | | GA ARRAY STORAGE = 3200 bytes | | | | TOTAL ESTIMATED MEMORY USAGE = 1412744 bytes | | | --------------------------------------------------------------------- WARNING: C -N -CT-C dihedral is missing 4 data points in the range 1.8850 to 3.1416 radians. WARNING: N -CT-C -N dihedral is missing 5 data points in the range 1.8850 to 3.1416 radians. WARNING: Insufficient dihedral information in sample structures. Your settings require at least 10 samples with data at least every 0.314 radians (18.00 degrees). Either 1) Add the missing input data or 2) Set DIHEDRAL_SPAN to a smaller value or 3) Set BOUNDS_CHECK to warn (not recommended). Please read the help and/or documentation. ------------------------------- INITIAL PARAMETERS -------------------------------- --------------------- ( printing only parameters to be fit ) ---------------------- Prmtop K ------------------ -------- a.prmtop -466382.135709 kcal/mol b.prmtop -416993.330876 kcal/mol c.prmtop -441694.818593 kcal/mol *(C -N -CT-C ) Kp = 1.7000 kcal/mol, Np = 1.0000, Phase = 0.0000 Deg *(C -N -CT-C ) Kp = 2.0000 kcal/mol, Np = 2.0000, Phase = 0.0000 Deg *(C -N -CT-C ) Kp = 0.0000 kcal/mol, Np = 3.0000, Phase = 0.0000 Deg *(C -N -CT-C ) Kp = 0.0000 kcal/mol, Np = 4.0000, Phase = 0.0000 Deg *(N -CT-C -N ) Kp = 0.8000 kcal/mol, Np = 1.0000, Phase = 180.0001 Deg *(N -CT-C -N ) Kp = 0.8500 kcal/mol, Np = 2.0000, Phase = 180.0001 Deg *(N -CT-C -N ) Kp = 0.0000 kcal/mol, Np = 3.0000, Phase = 180.0001 Deg *(N -CT-C -N ) Kp = 0.0000 kcal/mol, Np = 4.0000, Phase = 0.0000 Deg ----------------------------------------------------------------------------------- Sum of squares for initial parameters = 64137.7263450922 kcal^2/mol^2 R^2 value for initial parameters = 0.999757 Calculated energy with initial parameters for structure 1 = -466354.222831 KCal/mol Actual energy for structure 1 should be = -466326.093676 KCal/mol --------------------------GENETIC ALGORITHM MINIMISATION --------------------------- Minimising function SUM_SQUARES_AMBER_STANDARD, using the GENETIC ALGORITHM Running SIMPLEX REFINEMENT every 5 converged gen, then break for 5 ------------------------------------------------------------------------------------- GENERATIONS_TO_CONVERGE = 20 MAX_GENERATIONS = 10000 CONV_LIMIT = 1.00E+01 OPTIMIZATIONS = 50 PARENT_PERCENT = 0.25 SEARCH_SPACE = -1.00 MAX_GENERATIONS = 10000 ------------------------------------ CONVERGENCE ------------------------------------ Gen 0: Best= 165999.19541 Mean= 6.3164e+05 Elapsed= 0/3 Gen 1: Best= 130360.14504 Mean= 4.5228e+05 Elapsed= 1/3 Gen 2: Best= 80610.39410 Mean= 2.9872e+05 Elapsed= 2/3 Gen 3: Best= 71579.80794 Mean= 1.4591e+05 Conv= 0/20 Gen 4: Best= 66100.45147 Mean= 1.0561e+05 Conv= 0/20 Gen 5: Best= 59355.18768 Mean= 87101 Conv= 0/20 Gen 6: Best= 53900.96438 Mean= 71796 Conv= 0/20 Gen 7: Best= 53900.96438 Mean= 61247 Conv= 1/20 Gen 8: Best= 52663.36185 Mean= 56816 Conv= 0/20 Gen 9: Best= 51600.67237 Mean= 54266 Conv= 0/20 Gen 10: Best= 51334.60400 Mean= 52559 Conv= 0/20 Gen 11: Best= 50574.74197 Mean= 51744 Conv= 0/20 Gen 12: Best= 50366.60435 Mean= 51133 Conv= 0/20 Gen 13: Best= 49917.26714 Mean= 50734 Conv= 0/20 Gen 14: Best= 49690.09528 Mean= 50320 Conv= 0/20 Gen 15: Best= 49538.64715 Mean= 49926 Conv= 0/20 Gen 16: Best= 49396.72514 Mean= 49711 Conv= 0/20 Gen 17: Best= 49211.64496 Mean= 49540 Conv= 0/20 Gen 18: Best= 48984.25246 Mean= 49375 Conv= 0/20 Gen 19: Best= 48905.61218 Mean= 49164 Conv= 0/20 Gen 20: Best= 48726.69766 Mean= 48995 Conv= 0/20 Gen 21: Best= 48625.12134 Mean= 48898 Conv= 0/20 Gen 22: Best= 48585.87048 Mean= 48767 Conv= 0/20 Gen 23: Best= 48536.44844 Mean= 48660 Conv= 0/20 Gen 24: Best= 48434.97058 Mean= 48587 Conv= 0/20 Gen 25: Best= 48386.27796 Mean= 48501 Conv= 0/20 Gen 26: Best= 48346.28242 Mean= 48437 Conv= 0/20 Gen 27: Best= 48308.50154 Mean= 48372 Conv= 0/20 Gen 28: Best= 48242.40305 Mean= 48325 Conv= 0/20 Gen 29: Best= 48193.75252 Mean= 48282 Conv= 0/20 Gen 30: Best= 48144.35107 Mean= 48230 Conv= 0/20 Gen 31: Best= 48137.70802 Mean= 48195 Conv= 0/20 Gen 32: Best= 48123.57546 Mean= 48166 Conv= 0/20 Gen 33: Best= 48094.97052 Mean= 48138 Conv= 0/20 Gen 34: Best= 48080.44415 Mean= 48115 Conv= 0/20 Gen 35: Best= 48070.69941 Mean= 48095 Conv= 0/20 Gen 36: Best= 48058.34330 Mean= 48077 Conv= 0/20 Gen 37: Best= 48051.49960 Mean= 48068 Conv= 0/20 Gen 38: Best= 48049.01632 Mean= 48060 Conv= 0/20 Gen 39: Best= 48040.65097 Mean= 48052 Conv= 0/20 Gen 40: Best= 48032.93364 Mean= 48048 Conv= 0/20 Gen 41: Best= 48030.15436 Mean= 48039 Conv= 0/20 Gen 42: Best= 48020.18634 Mean= 48033 Conv= 0/20 Gen 43: Best= 48019.02710 Mean= 48029 Conv= 0/20 Gen 44: Best= 48013.37914 Mean= 48024 Conv= 0/20 Gen 45: Best= 48009.93132 Mean= 48018 Conv= 0/20 Gen 46: Best= 48008.42271 Mean= 48013 Conv= 0/20 Gen 47: Best= 48005.29159 Mean= 48010 Conv= 0/20 Gen 48: Best= 48004.13945 Mean= 48008 Conv= 0/20 Gen 49: Best= 48002.70323 Mean= 48005 Conv= 0/20 Gen 50: Best= 48001.60172 Mean= 48004 Conv= 0/20 Gen 51: Best= 48001.22865 Mean= 48003 Conv= 0/20 Gen 52: Best= 47998.37865 Mean= 48002 Conv= 0/20 Gen 53: Best= 47997.39773 Mean= 48000 Conv= 0/20 Gen 54: Best= 47996.45475 Mean= 47999 Conv= 0/20 Gen 55: Best= 47995.44615 Mean= 47998 Conv= 0/20 Gen 56: Best= 47994.56911 Mean= 47996 Conv= 0/20 Gen 57: Best= 47993.65730 Mean= 47995 Conv= 0/20 Gen 58: Best= 47993.51489 Mean= 47994 Conv= 0/20 Gen 59: Best= 47992.81347 Mean= 47994 Conv= 0/20 Gen 60: Best= 47992.59378 Mean= 47993 Conv= 0/20 Gen 61: Best= 47991.87840 Mean= 47993 Conv= 0/20 Gen 62: Best= 47991.81453 Mean= 47992 Conv= 0/20 Gen 63: Best= 47991.42569 Mean= 47992 Conv= 0/20 Gen 64: Best= 47990.97343 Mean= 47992 Conv= 0/20 Gen 65: Best= 47990.16201 Mean= 47991 Conv= 0/20 Gen 66: Best= 47990.08573 Mean= 47991 Conv= 0/20 Gen 67: Best= 47989.80694 Mean= 47990 Conv= 0/20 Gen 68: Best= 47989.76294 Mean= 47990 Conv= 0/20 Gen 69: Best= 47989.34177 Mean= 47990 Conv= 0/20 Gen 70: Best= 47989.29900 Mean= 47990 Conv= 0/20 Gen 71: Best= 47989.13994 Mean= 47989 Conv= 0/20 Gen 72: Best= 47988.99768 Mean= 47989 Conv= 0/20 Gen 73: Best= 47988.92557 Mean= 47989 Conv= 0/20 Gen 74: Best= 47988.74901 Mean= 47989 Conv= 0/20 Gen 75: Best= 47988.67473 Mean= 47989 Conv= 0/20 Gen 76: Best= 47988.61726 Mean= 47989 Conv= 0/20 Gen 77: Best= 47988.49457 Mean= 47989 Conv= 0/20 Gen 78: Best= 47988.48705 Mean= 47989 Conv= 0/20 Gen 79: Best= 47988.34588 Mean= 47989 Conv= 0/20 Gen 80: Best= 47988.34308 Mean= 47989 Conv= 0/20 Gen 81: Best= 47988.23826 Mean= 47988 Conv= 0/20 Gen 82: Best= 47988.23826 Mean= 47988 Conv= 1/20 Gen 83: Best= 47988.20592 Mean= 47988 Conv= 0/20 Gen 84: Best= 47988.09043 Mean= 47988 Conv= 0/20 Gen 85: Best= 47988.09043 Mean= 47988 Conv= 1/20 Gen 86: Best= 47988.04924 Mean= 47988 Conv= 0/20 Gen 87: Best= 47988.01065 Mean= 47988 Conv= 0/20 Gen 88: Best= 47988.01065 Mean= 47988 Conv= 1/20 Gen 89: Best= 47988.00548 Mean= 47988 Conv= 0/20 Gen 90: Best= 47988.00379 Mean= 47988 Conv= 0/20 Gen 91: Best= 47987.95886 Mean= 47988 Conv= 0/20 Gen 92: Best= 47987.95857 Mean= 47988 Conv= 0/20 Gen 93: Best= 47987.94676 Mean= 47988 Conv= 0/20 Gen 94: Best= 47987.94055 Mean= 47988 Conv= 0/20 Gen 95: Best= 47987.94043 Mean= 47988 Conv= 0/20 Gen 96: Best= 47987.92690 Mean= 47988 Conv= 0/20 Gen 97: Best= 47987.91662 Mean= 47988 Conv= 0/20 Gen 98: Best= 47987.90752 Mean= 47988 Conv= 0/20 Gen 99: Best= 47987.89710 Mean= 47988 Conv= 0/20 Gen 100: Best= 47987.89710 Mean= 47988 Conv= 1/20 Gen 101: Best= 47987.88602 Mean= 47988 Conv= 0/20 Gen 102: Best= 47987.87658 Mean= 47988 Conv= 0/20 Gen 103: Best= 47987.87658 Mean= 47988 Conv= 1/20 Gen 104: Best= 47987.87469 Mean= 47988 Conv= 0/20 Gen 105: Best= 47987.87057 Mean= 47988 Conv= 0/20 Gen 106: Best= 47987.86617 Mean= 47988 Conv= 0/20 Gen 107: Best= 47987.86411 Mean= 47988 Conv= 0/20 Gen 108: Best= 47987.85899 Mean= 47988 Conv= 0/20 Gen 109: Best= 47987.85899 Mean= 47988 Conv= 1/20 Gen 110: Best= 47987.85402 Mean= 47988 Conv= 0/20 Gen 111: Best= 47987.84589 Mean= 47988 Conv= 0/20 Gen 112: Best= 47987.84521 Mean= 47988 Conv= 0/20 Gen 113: Best= 47987.84521 Mean= 47988 Conv= 1/20 Gen 114: Best= 47987.84499 Mean= 47988 Conv= 0/20 Gen 115: Best= 47987.84357 Mean= 47988 Conv= 0/20 Gen 116: Best= 47987.84190 Mean= 47988 Conv= 0/20 Gen 117: Best= 47987.84106 Mean= 47988 Conv= 0/20 Gen 118: Best= 47987.84039 Mean= 47988 Conv= 0/20 Gen 119: Best= 47987.83964 Mean= 47988 Conv= 0/20 Gen 120: Best= 47987.83835 Mean= 47988 Conv= 0/20 Gen 121: Best= 47987.83834 Mean= 47988 Conv= 1/20 Gen 122: Best= 47987.83808 Mean= 47988 Conv= 0/20 Gen 123: Best= 47987.83780 Mean= 47988 Conv= 0/20 Gen 124: Best= 47987.83753 Mean= 47988 Conv= 0/20 Gen 125: Best= 47987.83753 Mean= 47988 Conv= 1/20 Gen 126: Best= 47987.83631 Mean= 47988 Conv= 0/20 Gen 127: Best= 47987.83631 Mean= 47988 Conv= 1/20 Gen 128: Best= 47987.83631 Mean= 47988 Conv= 2/20 Gen 129: Best= 47987.83622 Mean= 47988 Conv= 3/20 Gen 130: Best= 47987.83621 Mean= 47988 Conv= 4/20 Gen 131: Best= 47987.83612 Mean= 47988 Conv= 5/20 Gen 132: Best= 40471.35712 Mean= 47540 Conv= 0/20 Gen 133: Best= 40471.35712 Mean= 47966 Conv= 1/20 Gen 134: Best= 40471.35712 Mean= 46893 Conv= 2/20 Gen 135: Best= 40471.35712 Mean= 43511 Conv= 3/20 Gen 136: Best= 40471.35712 Mean= 42218 Conv= 4/20 Gen 137: Best= 40471.35712 Mean= 41017 Conv= 5/20 Gen 138: Best= 40471.35712 Mean= 40669 Conv= 6/20 Gen 139: Best= 40464.08131 Mean= 40569 Conv= 0/20 Gen 140: Best= 40464.08131 Mean= 40499 Conv= 1/20 Gen 141: Best= 40464.08131 Mean= 40480 Conv= 2/20 Gen 142: Best= 40464.08131 Mean= 40483 Conv= 3/20 Gen 143: Best= 40464.08131 Mean= 40480 Conv= 4/20 Gen 144: Best= 40464.08131 Mean= 40477 Conv= 5/20 Gen 145: Best= 40464.08131 Mean= 40477 Conv= 6/20 Gen 146: Best= 40464.08131 Mean= 40476 Conv= 7/20 Gen 147: Best= 40464.08131 Mean= 40478 Conv= 8/20 Gen 148: Best= 40464.08131 Mean= 40477 Conv= 9/20 Gen 149: Best= 40464.08131 Mean= 40474 Conv= 10/20 Gen 150: Best= 40464.08131 Mean= 40479 Conv= 11/20 Gen 151: Best= 40464.08131 Mean= 40481 Conv= 12/20 Gen 152: Best= 40464.08131 Mean= 40475 Conv= 13/20 Gen 153: Best= 40464.08131 Mean= 40481 Conv= 14/20 Gen 154: Best= 40464.08131 Mean= 40475 Conv= 15/20 Gen 155: Best= 40464.08131 Mean= 40481 Conv= 16/20 Gen 156: Best= 40464.08131 Mean= 40488 Conv= 17/20 Gen 157: Best= 40464.08131 Mean= 40473 Conv= 18/20 Gen 158: Best= 40464.08131 Mean= 40479 Conv= 19/20 Gen 159: Best= 40464.08131 Mean= 40480 Conv= 20/20 | Took 160 generations to converge. ------------------------------- FINAL PARAMETERS --------------------------------- --------------------- ( printing only parameters to be fit ) --------------------- Prmtop K ------------------ -------- a.prmtop -466382.135709 kcal/mol b.prmtop -416993.330876 kcal/mol c.prmtop -441694.818593 kcal/mol *(C -N -CT-C ) Kp = -2.0548 kcal/mol, Np = 1.0000, Phase = 0.0000 Deg *(C -N -CT-C ) Kp = -5.3784 kcal/mol, Np = 2.0000, Phase = 0.0000 Deg *(C -N -CT-C ) Kp = -8.0264 kcal/mol, Np = 3.0000, Phase = 0.0000 Deg *(C -N -CT-C ) Kp = 1.6187 kcal/mol, Np = 4.0000, Phase = 0.0000 Deg *(N -CT-C -N ) Kp = -1.6315 kcal/mol, Np = 1.0000, Phase = 180.0001 Deg *(N -CT-C -N ) Kp = 2.7000 kcal/mol, Np = 2.0000, Phase = 180.0001 Deg *(N -CT-C -N ) Kp = 4.8765 kcal/mol, Np = 3.0000, Phase = 180.0001 Deg *(N -CT-C -N ) Kp = 8.8604 kcal/mol, Np = 4.0000, Phase = 0.0000 Deg ---------------------------------------------------------------------------------- | Called the fitness function 11779 times. Function value with fitted parameters = 40464.0813, R^2 = 0.9998 Calculated energy with fitted parameters for structure 1 = 20.2496 KCal/mol * Saving ffrcmod file to frcmod * Saving energy file with 20 structures to a.prmtop_multi_energy.dat * Saving energy file with 20 structures to b.prmtop_multi_energy.dat * Saving energy file with 20 structures to c.prmtop_multi_energy.dat * Result passed angle validity check. * Result passed bond validity check. | Program Execution Completed at: Mon Jun 16 15:45:00 2014 | Elapsed Time = 45.00 seconds *************************************************************************************