***************************************************** * 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: | Fri Jun 13 13:22:16 2014 | | Random seed = 1402690936 Reading job control file: fit_K.in Job Control: Read a total of 8 lines from job_control file. 7 options set. Reading prmtop file : a.prmtop 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 = SIMPLEX | | Function to be Fit = SUM_SQUARES_AMBER_STANDARD | | | | Terms to be fit: | | K = 1, UNIQUE_BONDS = 8, UNIQUE ANGLES = 16 | | UNIQUE DIHEDRALS = 23 TOTAL DIHEDRAL TERMS = 38 | | NBONDS = 31, NANGLES = 54, NDIHEDRALS = 105 | | Total dimensions of fit = 1 | | | | Sample structures for least squares fit = 20 | | | | | | Energy Correction Term (K) = TO BE FIT | | | | BONDFC_dx = 5.0000 | | BONDEQ_dx = 0.0200 | | ANGLEFC_dx = 1.0000 | | ANGLEEQ_dx = 0.0500 | | DIHEDRALBH_dx = 0.2000 | | DIHEDRALN_dx = 0.0100 | | DIHEDRALG_dx = 0.0500 | | K_dx = 10.0000 | | | | Convergence requested to within 1.0000E-15 | | | | Estimate Memory Usage (per cpu): | | Coordinate info will be read from disk as required. | | OPTION STORAGE = 64 bytes | | PRMTOP STORAGE = 502650 bytes | | COORDINATE STORAGE = 16520 bytes | | SIMPLEX ARRAY STORAGE = 168 bytes | | | | TOTAL ESTIMATED MEMORY USAGE = 519402 bytes | | | --------------------------------------------------------------------- * Input structures passed dihedral span check. ------------------------------- INITIAL PARAMETERS -------------------------------- Parameters for force field equation: AMBER_STANDARD: (* means parameter is NOT constant during fit) *K = 0.000000 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 = 4352905409221.3247070312 kcal^2/mol^2 R^2 value for initial parameters = 0.944033 Calculated energy with initial parameters for structure 1 = 27.912878 KCal/mol Actual energy for structure 1 should be = -466326.093676 KCal/mol --------------------------------- SIMPLEX MINIMISATION ---------------------------- Minimising function SUM_SQUARES_AMBER_STANDARD, using the SIMPLEX METHOD -------------------------------------- CONVERGENCE -------------------------------- Step 0: Conv= 4.3174E-05 min=4352905409221.3247,max=4353093343548.0576 avg4352999376384.6914 Step 1: Conv= 3.1213E-02 min=3793662.6950 max=3913951.0252 avg=3853806.8601 Step 2: Conv= 2.5056E-16 min=3717020.1590 max=3717020.1590 avg=3717020.1590 ----------------------------------------------------------------------------------- Convergence ratio of 2.5056E-16 is better than convergence criteria of 1.0000E-15. Function Converged - Total function evaluations = 104 Convergence to 1.0000E-15 in Simplex routine achieved after 50 cycles. (25 INNER x 2 OUTER CYCLES) ------------------------------- FINAL PARAMETERS --------------------------------- Parameters for force field equation: AMBER_STANDARD: (* means parameter is NOT constant during fit) *K = -466524.473749 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 105 times. Function value with fitted parameters = 3717020.1590, R^2 = 0.9440 Calculated energy with fitted parameters for structure 1 = 27.9129 KCal/mol * Saving energy file with 20 structures to fita.dat * Result passed angle validity check. * Result passed bond validity check. | Program Execution Completed at: Fri Jun 13 13:22:17 2014 | Elapsed Time = 1.00 seconds *************************************************************************************