***************************************************** * 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: | Wed Jun 11 13:52:06 2014 | | Random seed = 1402519926 Reading job control file: job_scatterplots.in Job Control: Read a total of 10 lines from job_control file. 7 options set. Reading prmtop file : a.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. Reading mdcrd file: A_valid_structures.mdcrd Reading mdcrd file : A_valid_structures.mdcrd Coordinate file passed format check Reading energy file or directory : quantum_A.dat --------------------------------------------------------------------- | OPTIONS SUMMARY | | --------------- | | Summary of Run Type Options: | | Run Mode = FIT, Minimiser = UNKNOWN | | 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 = 20 | | | | | | Energy Correction Term (K) = -466524.47375400 | | | | | | Estimate Memory Usage (per cpu): | | Coordinate info will be read from disk as required. | | OPTION STORAGE = 74 bytes | | PRMTOP STORAGE = 502650 bytes | | COORDINATE STORAGE = 16520 bytes | | | | TOTAL ESTIMATED MEMORY USAGE = 519244 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 -------------------------------- Parameters for force field equation: AMBER_STANDARD: (* means parameter is NOT constant during fit) K = -466524.473754 kcal/mol (CT-HC) Kr = 340.0000 kcal/(mol A)^2, r_eq = 1.0900 A (CT-H1) Kr = 340.0000 kcal/(mol A)^2, r_eq = 1.0900 A (N -H ) Kr = 434.0000 kcal/(mol A)^2, r_eq = 1.0100 A (C -O ) Kr = 570.0000 kcal/(mol A)^2, r_eq = 1.2290 A (C -N ) Kr = 490.0000 kcal/(mol A)^2, r_eq = 1.3350 A (CT-C ) Kr = 317.0000 kcal/(mol A)^2, r_eq = 1.5220 A (CT-CT) Kr = 310.0000 kcal/(mol A)^2, r_eq = 1.5260 A (N -CT) Kr = 337.0000 kcal/(mol A)^2, r_eq = 1.4490 A (C -N -H ) Kt = 50.0000 kcal/(mol rad)^2, th_eq = 120.0001 deg (HC-CT-C ) Kt = 50.0000 kcal/(mol rad)^2, th_eq = 109.5000 deg (HC-CT-HC) Kt = 35.0000 kcal/(mol rad)^2, th_eq = 109.5000 deg (H1-CT-CT) Kt = 50.0000 kcal/(mol rad)^2, th_eq = 109.5000 deg (H1-CT-C ) Kt = 50.0000 kcal/(mol rad)^2, th_eq = 109.5000 deg (CT-CT-HC) Kt = 50.0000 kcal/(mol rad)^2, th_eq = 109.5000 deg (H -N -CT) Kt = 50.0000 kcal/(mol rad)^2, th_eq = 118.0401 deg (N -CT-H1) Kt = 50.0000 kcal/(mol rad)^2, th_eq = 109.5000 deg (H1-CT-H1) Kt = 35.0000 kcal/(mol rad)^2, th_eq = 109.5000 deg (O -C -N ) Kt = 80.0000 kcal/(mol rad)^2, th_eq = 122.9001 deg (C -N -CT) Kt = 50.0000 kcal/(mol rad)^2, th_eq = 121.9001 deg (CT-C -O ) Kt = 80.0000 kcal/(mol rad)^2, th_eq = 120.4001 deg (CT-C -N ) Kt = 70.0000 kcal/(mol rad)^2, th_eq = 116.6000 deg (CT-CT-C ) Kt = 63.0000 kcal/(mol rad)^2, th_eq = 111.1000 deg (N -CT-CT) Kt = 80.0000 kcal/(mol rad)^2, th_eq = 109.7000 deg (N -CT-C ) Kt = 63.0000 kcal/(mol rad)^2, th_eq = 110.1000 deg (O -C -N -H ) Kp = 2.0000 kcal/mol, Np = 1.0000, Phase = 0.0000 Deg (O -C -N -H ) Kp = 2.5000 kcal/mol, Np = 2.0000, Phase = 180.0001 Deg (C -N -CT-H1) Kp = 0.0000 kcal/mol, Np = 2.0000, Phase = 0.0000 Deg (HC-CT-C -O ) Kp = 0.8000 kcal/mol, Np = 1.0000, Phase = 0.0000 Deg (HC-CT-C -O ) Kp = 0.0000 kcal/mol, Np = 2.0000, Phase = 0.0000 Deg (HC-CT-C -O ) Kp = 0.0800 kcal/mol, Np = 3.0000, Phase = 180.0001 Deg (HC-CT-C -N ) Kp = 0.0000 kcal/mol, Np = 2.0000, Phase = 0.0000 Deg (CT-C -N -H ) Kp = 2.5000 kcal/mol, Np = 2.0000, Phase = 180.0001 Deg (HC-CT-CT-C ) Kp = 0.1556 kcal/mol, Np = 3.0000, Phase = 0.0000 Deg (H1-CT-CT-HC) Kp = 0.1556 kcal/mol, Np = 3.0000, Phase = 0.0000 Deg (H1-CT-C -O ) Kp = 0.8000 kcal/mol, Np = 1.0000, Phase = 0.0000 Deg (H1-CT-C -O ) Kp = 0.0000 kcal/mol, Np = 2.0000, Phase = 0.0000 Deg (H1-CT-C -O ) Kp = 0.0800 kcal/mol, Np = 3.0000, Phase = 180.0001 Deg (H1-CT-C -N ) Kp = 0.0000 kcal/mol, Np = 2.0000, Phase = 0.0000 Deg (H -N -CT-H1) Kp = 0.0000 kcal/mol, Np = 2.0000, Phase = 0.0000 Deg (H -N -CT-CT) Kp = 0.0000 kcal/mol, Np = 2.0000, Phase = 0.0000 Deg (H -N -CT-C ) Kp = 0.0000 kcal/mol, Np = 2.0000, Phase = 0.0000 Deg (N -CT-CT-HC) Kp = 0.1556 kcal/mol, Np = 3.0000, Phase = 0.0000 Deg IMP (C -CT-N -H ) Kp = 1.1000 kcal/mol, Np = 2.0000, Phase = 180.0001 Deg (O -C -N -CT) Kp = 2.5000 kcal/mol, Np = 2.0000, Phase = 180.0001 Deg (C -N -CT-CT) Kp = 0.5300 kcal/mol, Np = 1.0000, Phase = 0.0000 Deg (C -N -CT-CT) Kp = 0.0000 kcal/mol, Np = 2.0000, Phase = 0.0000 Deg (C -N -CT-CT) Kp = 0.1500 kcal/mol, Np = 3.0000, Phase = 180.0001 Deg (C -N -CT-CT) Kp = 0.5000 kcal/mol, Np = 4.0000, Phase = 180.0001 Deg (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 (CT-C -N -CT) Kp = 2.5000 kcal/mol, Np = 2.0000, Phase = 180.0001 Deg (CT-CT-C -O ) Kp = 0.0000 kcal/mol, Np = 2.0000, Phase = 0.0000 Deg (CT-CT-C -N ) Kp = 0.0700 kcal/mol, Np = 2.0000, Phase = 0.0000 Deg (CT-CT-C -N ) Kp = 0.1000 kcal/mol, Np = 4.0000, Phase = 0.0000 Deg (N -CT-C -O ) Kp = 0.0000 kcal/mol, Np = 2.0000, 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 IMP (CT-N -C -O ) Kp = 10.5000 kcal/mol, Np = 2.0000, Phase = 180.0001 Deg ----------------------------------------------------------------------------------- Sum of squares for initial parameters = 3717020.1589778299 kcal^2/mol^2 R^2 value for initial parameters = 0.944033 Calculated energy with initial parameters for structure 1 = -466496.560876 KCal/mol Actual energy for structure 1 should be = -466326.093676 KCal/mol ------------------------------- FINAL PARAMETERS --------------------------------- Parameters for force field equation: AMBER_STANDARD: (* means parameter is NOT constant during fit) K = -466524.473754 kcal/mol (CT-HC) Kr = 340.0000 kcal/(mol A)^2, r_eq = 1.0900 A (CT-H1) Kr = 340.0000 kcal/(mol A)^2, r_eq = 1.0900 A (N -H ) Kr = 434.0000 kcal/(mol A)^2, r_eq = 1.0100 A (C -O ) Kr = 570.0000 kcal/(mol A)^2, r_eq = 1.2290 A (C -N ) Kr = 490.0000 kcal/(mol A)^2, r_eq = 1.3350 A (CT-C ) Kr = 317.0000 kcal/(mol A)^2, r_eq = 1.5220 A (CT-CT) Kr = 310.0000 kcal/(mol A)^2, r_eq = 1.5260 A (N -CT) Kr = 337.0000 kcal/(mol A)^2, r_eq = 1.4490 A (C -N -H ) Kt = 50.0000 kcal/(mol rad)^2, th_eq = 120.0001 deg (HC-CT-C ) Kt = 50.0000 kcal/(mol rad)^2, th_eq = 109.5000 deg (HC-CT-HC) Kt = 35.0000 kcal/(mol rad)^2, th_eq = 109.5000 deg (H1-CT-CT) Kt = 50.0000 kcal/(mol rad)^2, th_eq = 109.5000 deg (H1-CT-C ) Kt = 50.0000 kcal/(mol rad)^2, th_eq = 109.5000 deg (CT-CT-HC) Kt = 50.0000 kcal/(mol rad)^2, th_eq = 109.5000 deg (H -N -CT) Kt = 50.0000 kcal/(mol rad)^2, th_eq = 118.0401 deg (N -CT-H1) Kt = 50.0000 kcal/(mol rad)^2, th_eq = 109.5000 deg (H1-CT-H1) Kt = 35.0000 kcal/(mol rad)^2, th_eq = 109.5000 deg (O -C -N ) Kt = 80.0000 kcal/(mol rad)^2, th_eq = 122.9001 deg (C -N -CT) Kt = 50.0000 kcal/(mol rad)^2, th_eq = 121.9001 deg (CT-C -O ) Kt = 80.0000 kcal/(mol rad)^2, th_eq = 120.4001 deg (CT-C -N ) Kt = 70.0000 kcal/(mol rad)^2, th_eq = 116.6000 deg (CT-CT-C ) Kt = 63.0000 kcal/(mol rad)^2, th_eq = 111.1000 deg (N -CT-CT) Kt = 80.0000 kcal/(mol rad)^2, th_eq = 109.7000 deg (N -CT-C ) Kt = 63.0000 kcal/(mol rad)^2, th_eq = 110.1000 deg (O -C -N -H ) Kp = 2.0000 kcal/mol, Np = 1.0000, Phase = 0.0000 Deg (O -C -N -H ) Kp = 2.5000 kcal/mol, Np = 2.0000, Phase = 180.0001 Deg (C -N -CT-H1) Kp = 0.0000 kcal/mol, Np = 2.0000, Phase = 0.0000 Deg (HC-CT-C -O ) Kp = 0.8000 kcal/mol, Np = 1.0000, Phase = 0.0000 Deg (HC-CT-C -O ) Kp = 0.0000 kcal/mol, Np = 2.0000, Phase = 0.0000 Deg (HC-CT-C -O ) Kp = 0.0800 kcal/mol, Np = 3.0000, Phase = 180.0001 Deg (HC-CT-C -N ) Kp = 0.0000 kcal/mol, Np = 2.0000, Phase = 0.0000 Deg (CT-C -N -H ) Kp = 2.5000 kcal/mol, Np = 2.0000, Phase = 180.0001 Deg (HC-CT-CT-C ) Kp = 0.1556 kcal/mol, Np = 3.0000, Phase = 0.0000 Deg (H1-CT-CT-HC) Kp = 0.1556 kcal/mol, Np = 3.0000, Phase = 0.0000 Deg (H1-CT-C -O ) Kp = 0.8000 kcal/mol, Np = 1.0000, Phase = 0.0000 Deg (H1-CT-C -O ) Kp = 0.0000 kcal/mol, Np = 2.0000, Phase = 0.0000 Deg (H1-CT-C -O ) Kp = 0.0800 kcal/mol, Np = 3.0000, Phase = 180.0001 Deg (H1-CT-C -N ) Kp = 0.0000 kcal/mol, Np = 2.0000, Phase = 0.0000 Deg (H -N -CT-H1) Kp = 0.0000 kcal/mol, Np = 2.0000, Phase = 0.0000 Deg (H -N -CT-CT) Kp = 0.0000 kcal/mol, Np = 2.0000, Phase = 0.0000 Deg (H -N -CT-C ) Kp = 0.0000 kcal/mol, Np = 2.0000, Phase = 0.0000 Deg (N -CT-CT-HC) Kp = 0.1556 kcal/mol, Np = 3.0000, Phase = 0.0000 Deg IMP (C -CT-N -H ) Kp = 1.1000 kcal/mol, Np = 2.0000, Phase = 180.0001 Deg (O -C -N -CT) Kp = 2.5000 kcal/mol, Np = 2.0000, Phase = 180.0001 Deg (C -N -CT-CT) Kp = 0.5300 kcal/mol, Np = 1.0000, Phase = 0.0000 Deg (C -N -CT-CT) Kp = 0.0000 kcal/mol, Np = 2.0000, Phase = 0.0000 Deg (C -N -CT-CT) Kp = 0.1500 kcal/mol, Np = 3.0000, Phase = 180.0001 Deg (C -N -CT-CT) Kp = 0.5000 kcal/mol, Np = 4.0000, Phase = 180.0001 Deg (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 (CT-C -N -CT) Kp = 2.5000 kcal/mol, Np = 2.0000, Phase = 180.0001 Deg (CT-CT-C -O ) Kp = 0.0000 kcal/mol, Np = 2.0000, Phase = 0.0000 Deg (CT-CT-C -N ) Kp = 0.0700 kcal/mol, Np = 2.0000, Phase = 0.0000 Deg (CT-CT-C -N ) Kp = 0.1000 kcal/mol, Np = 4.0000, Phase = 0.0000 Deg (N -CT-C -O ) Kp = 0.0000 kcal/mol, Np = 2.0000, 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 IMP (CT-N -C -O ) Kp = 10.5000 kcal/mol, Np = 2.0000, Phase = 180.0001 Deg ---------------------------------------------------------------------------------- | Called the fitness function 1 times. Function value with fitted parameters = 3717020.1590, R^2 = 0.9440 Calculated energy with fitted parameters for structure 1 = 27.9129 KCal/mol * Result passed angle validity check. * Result passed bond validity check. | Program Execution Completed at: Wed Jun 11 13:52:06 2014 | Elapsed Time = 0.00 seconds *************************************************************************************