***************************************************** * 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: | Tue Jun 10 16:13:24 2014 | | Random seed = 1402442004 PARAMFIT SETTINGS WIZARD ------------------------ Enter a job control filename to save settings as, or hit enter > Not saving job control settings Which format is your coordinate file in? 1) Trajectory (.mdcrd,.inpcrd) 2) Restart (.rst, .restart) 1 What type of job do you want to run? 1) Create input files for quantum program 2) Set which parameters to fit 3) Conduct a fit 2 Enter a file name to define the parameter list in: > prms.in Do you want to save scatterplots of bonds, angles, and dihedrals in the input conformations? 1) Yes 2) No > 2 Successfully set options! Reading prmtop file : a.prmtop Would you like to optimise any bond parameters? (y/n): n Would you like to optimise any angle parameters? (y/n): n Would you like to optimise any dihedral parameters? (y/n): y - Any dihedral KP? (y/n): y - Any dihedral NP? (y/n): n - Any dihedral PHASE? (y/n): n Fit Parameter: DIHEDRAL (O -C -N -H ) term 1 KP? (y/n): n Fit Parameter: DIHEDRAL (O -C -N -H ) term 2 KP? (y/n): n Fit Parameter: DIHEDRAL (C -N -CT-H1) term 1 KP? (y/n): n Fit Parameter: DIHEDRAL (HC-CT-C -O ) term 1 KP? (y/n): n Fit Parameter: DIHEDRAL (HC-CT-C -O ) term 2 KP? (y/n): n Fit Parameter: DIHEDRAL (HC-CT-C -O ) term 3 KP? (y/n): n Fit Parameter: DIHEDRAL (HC-CT-C -N ) term 1 KP? (y/n): n Fit Parameter: DIHEDRAL (CT-C -N -H ) term 1 KP? (y/n): n Fit Parameter: DIHEDRAL (HC-CT-CT-C ) term 1 KP? (y/n): n Fit Parameter: DIHEDRAL (H1-CT-CT-HC) term 1 KP? (y/n): n Fit Parameter: DIHEDRAL (H1-CT-C -O ) term 1 KP? (y/n): n Fit Parameter: DIHEDRAL (H1-CT-C -O ) term 2 KP? (y/n): n Fit Parameter: DIHEDRAL (H1-CT-C -O ) term 3 KP? (y/n): n Fit Parameter: DIHEDRAL (H1-CT-C -N ) term 1 KP? (y/n): n Fit Parameter: DIHEDRAL (H -N -CT-H1) term 1 KP? (y/n): n Fit Parameter: DIHEDRAL (H -N -CT-CT) term 1 KP? (y/n): n Fit Parameter: DIHEDRAL (H -N -CT-C ) term 1 KP? (y/n): n Fit Parameter: DIHEDRAL (N -CT-CT-HC) term 1 KP? (y/n): n Fit Parameter: IMPROPER DIHEDRAL (C -CT-N -H ) term 1 KP? (y/n): n Fit Parameter: DIHEDRAL (O -C -N -CT) term 1 KP? (y/n): n Fit Parameter: DIHEDRAL (C -N -CT-CT) term 1 KP? (y/n): n Fit Parameter: DIHEDRAL (C -N -CT-CT) term 2 KP? (y/n): n Fit Parameter: DIHEDRAL (C -N -CT-CT) term 3 KP? (y/n): n Fit Parameter: DIHEDRAL (C -N -CT-CT) term 4 KP? (y/n): n Fit Parameter: DIHEDRAL (C -N -CT-C ) term 1 KP? (y/n): y Fit Parameter: DIHEDRAL (C -N -CT-C ) term 2 KP? (y/n): y Fit Parameter: DIHEDRAL (C -N -CT-C ) term 3 KP? (y/n): y Fit Parameter: DIHEDRAL (C -N -CT-C ) term 4 KP? (y/n): y Fit Parameter: DIHEDRAL (CT-C -N -CT) term 1 KP? (y/n): n Fit Parameter: DIHEDRAL (CT-CT-C -O ) term 1 KP? (y/n): n Fit Parameter: DIHEDRAL (CT-CT-C -N ) term 1 KP? (y/n): n Fit Parameter: DIHEDRAL (CT-CT-C -N ) term 2 KP? (y/n): n Fit Parameter: DIHEDRAL (N -CT-C -O ) term 1 KP? (y/n): n Fit Parameter: DIHEDRAL (N -CT-C -N ) term 1 KP? (y/n): y Fit Parameter: DIHEDRAL (N -CT-C -N ) term 2 KP? (y/n): y Fit Parameter: DIHEDRAL (N -CT-C -N ) term 3 KP? (y/n): y Fit Parameter: DIHEDRAL (N -CT-C -N ) term 4 KP? (y/n): y Fit Parameter: IMPROPER DIHEDRAL (CT-N -C -O ) term 1 KP? (y/n): n Filename to be written is: prms.in 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. 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 * Successfully saved desired parameters. * Set runtype to FIT to do a fit with these parameters.