Hi Alechania,
Take all those data points you've collected and put them into mdgx for
parameter fitting instead. See this tutorial on how the process works and
where you can jump in.
http://ambermd.org/tutorials/advanced/tutorial32/index.php
If you have a trajectory of structures and a file full of energies, you can
perhaps jump in near the end. At the very least, if mdgx can't make sense
of your data and produce good parameters, then there is a deeper problem.
Also note that the mdgx &configs module is ideally suited for producing
poses of the molecule that at least pass muster with respect to an MM force
field, so near 100% of them should qualify for further investigation with
QM calculations. If you can offer mdgx a guess parameter set (say, the
default parameters from GAFF) and write that as a topology with tleap, then
you can make all sorts of manipulations and get a good sense of whether
what you are trying to sample is physically reasonable. The major
mathematical advancement of mdgx is that I've eliminated the need to fit
Paramfit's constant K: it is merely another variable in the least squares
optimization, so the program takes care of it and tells you what it did.
Dave
On Fri, Apr 27, 2018 at 10:29 AM, Alechania Misturini <alechaniam.gmail.com>
wrote:
> *Hello everyone, I'm a new user of Amber, and I'm experiencing some
> problems trying to obtain parameters for a siloxane unit (figure below),
> using paramfit.*
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> *I'm interested in parametrize some dihedral, angles and bonds, mainly
> involving Si, and the 4 atoms directly bonded in it (that were assigned
> with different atom types). I’m considering as initial parameters,
> analogous bonds, angles and dihedrals, changing Si for a c3 atom, and using
> these values defined in gaff.dat.Lennard-Jones values for Si was obtained
> from force field AMBER parm99, for docking
> (https://users.rcc.uchicago.edu/~yadunand/swift-k/bgq-
> swift/dock/vdw_AMBER_parm99.defn
> <https://users.rcc.uchicago.edu/~yadunand/swift-k/bgq-
> swift/dock/vdw_AMBER_parm99.defn>).Well,
> I try to follow paramfit tutorial, but, for my system, i'm obtaining really
> bad R^2 values for the first fitting of K (around 0.1), and for the
> subsequently parameter fit (the best one was 0.66).I try different
> approaches to solve this. 1) I improve my sampling, try 2 000 random
> conformations (resulting 341 good conformations), and 20 000 random
> conformations (resulting 3414 good conformations). In the last case, I find
> the "best" result for R^2 in K fitting (0.1284) and at the actual parameter
> fitting with R^2 = 0.6648.2) Another test was reducing the energy cutoff
> for removing bad structures. Previous calculations consider a 2000 kcal/mol
> cutoff, like in the tutorial. I reduce to 1500, cause some structures that
> pass this minima are yet bad conformations (and gives error in Gaussian
> calculation of single point, due overlapping atoms) -- and these ones are
> removed from my valid_structures.mdcrd with a script that I wrote. Reducing
> this cutoff shows worse results for R^2 (in both fitting K and parameters,
> I tested this for a 2 000 conformation system).3) Changing the level of
> theory. I started using b3lyp/6-31G* cause its the same level of theory
> used for resp calculation of charges. So, I tried with a greater basis set,
> 6-311G*, and still using a hybrid functional, but now, PBE0. The results
> were a little better, but, for 2 000 conformations, and 316 good ones
> (energy cutoff of 2000 kcal/mol), the fitting o K shows R^2 of 0.1034, and
> for the parameters R^2 = 0.6378.4) I tried to see the plots using
> plot_energy.x and scatterplots.sh, as the tutorial teach. Try to change the
> weight of some structures, but the R^2 gets even worse. It was difficult
> due the high number of conformations involved.- My QM calculations were
> just single points, I need to use a different approach? - There are some
> warnings about the parameters, that I try to solve by increasing the
> sampling, but this warnings are always present.How can I improve my
> fitting? Cause I don't have any other ideas to solve this and get a better
> fit. Thanks in advantage!Here are some informations about my system:*Atom
> types: (I’m using gaff)SI - Si atomJ3 - c3 bonded to SiQH - oh bonded to
> SiQS - os bonded to Si*My parameters to fit:# BOND INFORMATION:#### BOND
> REQ KR #### J3 hc 1 1 QH ho 1 1 c3
> J3 1 1 J3 SI 1 1 SI QH 1 1 SI QS 1
> 1 QS c3 1 1## ANGLE PARAMETERS:#### ANGLE KT THEQ
> #### c3 J3 hc 1 1 J3 c3 hc 1 1 hc J3 SI
> 1 1 hc J3 hc 1 1 SI QH ho 1 1 QS
> c3 h1 1 1 c3 c3 J3 1 1 c3 J3 SI 1 1
> J3 SI QH 1 1 J3 SI QS 1 1 SI QS c3
> 1 1 QH SI QS 1 1 QS SI QS 1 1## DIHEDRAL
> PARAMETERS:#### DIHEDRAL TERM KP NP PHASE #### c3 c3 J3 hc
> 0 1 1 1 J3 SI QH ho 0 1 1 1 J3 SI QH ho
> 1 1 1 1 hc c3 J3 hc 0 1 1 1 hc c3 J3 SI
> 0 1 1 1 hc J3 SI QH 0 1 1 1 hc J3 SI QH
> 1 1 1 1 hc J3 SI QS 0 1 1 1 hc J3 SI QS
> 1 1 1 1 SI QS c3 h1 0 1 1 1 QS SI QH ho
> 0 1 1 1 c3 c3 J3 SI 0 1 1 1 c3 c3 J3 SI
> 1 1 1 1 c3 c3 J3 SI 2 1 1 1 c3 J3 SI QH
> 0 1 1 1 c3 J3 SI QS 0 1 1 1 J3 SI QS c3
> 0 1 1 1 J3 SI QS c3 1 1 1 1 QH SI QS c3
> 0 1 1 1 QS SI QS c3 0 1 1 1 QS SI QS c3
> 1 1 1 1 QS SI QS c3 2 1 1 1*Outputs for a
> fitting with 20 000 structures, and 3179 good ones (cutoff of 2000 kcal/mol
> results in 3414 “good” structures, but 235 presented error reported
> previously, and were removed from valid.mdcrd)*Fitting K:
> *****************************************************
> * 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 Apr 24 16:00:09 2018|| Random seed =
> 1524596409 Reading job control file: fit_K_sil.in Job Control: Read a total
> of 12 lines from job_control file. 6 options set. Reading prmtop file :
> sil.prmtop Prmtop (unique): Found 10 unique bonds. Prmtop (unique):
> Found 16 unique angles. Prmtop (unique): Found 16 unique dihedrals.
> Prmtop (unique): Found 24 unique dihedral terms. Reading mdcrd file:
> sil_valid_structures.mdcrd Reading mdcrd file :
> sil_valid_structures.mdcrd Coordinate file passed format check Reading
> energy file or directory : energy_qm_sil.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 = 10, UNIQUE ANGLES = 16 | |
> UNIQUE DIHEDRALS = 16 TOTAL DIHEDRAL TERMS = 24 | |
> NBONDS = 22, NANGLES = 39, NDIHEDRALS = 57 | |
> Total dimensions of fit = 1 | |
> | |
> Sample structures for least squares fit = 3179 |
> | |
> | |
> | 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 = 67
> bytes | | PRMTOP STORAGE = 389242
> bytes | | COORDINATE STORAGE = 1958304
> bytes | | SIMPLEX ARRAY STORAGE = 168 bytes
> | |
> | | TOTAL
> ESTIMATED MEMORY USAGE = 2347781 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 (hc-c3) Kr =
> 330.6000 kcal/(mol A)^2, r_eq = 1.0969 A (J3-hc) Kr =
> 330.6000 kcal/(mol A)^2, r_eq = 1.0969 A (QH-ho) Kr =
> 371.4000 kcal/(mol A)^2, r_eq = 0.9730 A (c3-h1) Kr =
> 330.6000 kcal/(mol A)^2, r_eq = 1.0969 A (c3-c3) Kr =
> 300.9000 kcal/(mol A)^2, r_eq = 1.5375 A (c3-J3) Kr =
> 300.9000 kcal/(mol A)^2, r_eq = 1.5375 A (J3-SI) Kr =
> 206.0000 kcal/(mol A)^2, r_eq = 1.7800 A (SI-QH) Kr =
> 203.2000 kcal/(mol A)^2, r_eq = 1.7500 A (SI-QS) Kr =
> 599.8000 kcal/(mol A)^2, r_eq = 1.7580 A (QS-c3) Kr =
> 308.6000 kcal/(mol A)^2, r_eq = 1.4316 A (hc-c3-c3) Kt = 46.3400
> kcal/(mol rad)^2, th_eq = 109.8000 deg (hc-c3-hc) Kt = 39.4000
> kcal/(mol rad)^2, th_eq = 107.5800 deg (c3-J3-hc) Kt = 46.3400
> kcal/(mol rad)^2, th_eq = 109.8000 deg (J3-c3-hc) Kt = 46.3400
> kcal/(mol rad)^2, th_eq = 109.8000 deg (hc-J3-SI) Kt = 46.3400
> kcal/(mol rad)^2, th_eq = 109.8000 deg (hc-J3-hc) Kt = 39.4000
> kcal/(mol rad)^2, th_eq = 107.5800 deg (SI-QH-ho) Kt = 47.3800
> kcal/(mol rad)^2, th_eq = 107.2600 deg (QS-c3-h1) Kt = 50.8000
> kcal/(mol rad)^2, th_eq = 109.7800 deg (h1-c3-h1) Kt = 39.2400
> kcal/(mol rad)^2, th_eq = 108.4600 deg (c3-c3-J3) Kt = 62.8600
> kcal/(mol rad)^2, th_eq = 111.5100 deg (c3-J3-SI) Kt = 62.8600
> kcal/(mol rad)^2, th_eq = 111.5100 deg (J3-SI-QH) Kt = 67.4700
> kcal/(mol rad)^2, th_eq = 110.1900 deg (J3-SI-QS) Kt = 68.0000
> kcal/(mol rad)^2, th_eq = 107.9700 deg (SI-QS-c3) Kt = 62.7000
> kcal/(mol rad)^2, th_eq = 112.4800 deg (QH-SI-QS) Kt = 72.5800
> kcal/(mol rad)^2, th_eq = 109.3800 deg (QS-SI-QS) Kt = 72.7400
> kcal/(mol rad)^2, th_eq = 108.2900 deg (hc-c3-c3-J3) Kp = 0.1556
> kcal/mol, Np = 3.0000, Phase = 0.0000 Deg (hc-c3-c3-hc) Kp =
> 0.1500 kcal/mol, Np = 3.0000, Phase = 0.0000 Deg (c3-c3-J3-hc) Kp
> = 0.1600 kcal/mol, Np = 3.0000, Phase = 0.0000 Deg (J3-SI-QH-ho)
> Kp = 0.2500 kcal/mol, Np = 1.0000, Phase = 0.0000 Deg
> (J3-SI-QH-ho) Kp = 0.1600 kcal/mol, Np = 3.0000, Phase = 0.0000
> Deg (hc-c3-J3-hc) Kp = 0.1500 kcal/mol, Np = 3.0000, Phase =
> 0.0000 Deg (hc-c3-J3-SI) Kp = 0.1600 kcal/mol, Np = 3.0000, Phase
> = 0.0000 Deg (hc-J3-SI-QH) Kp = 0.2500 kcal/mol, Np = 1.0000,
> Phase = 0.0000 Deg (hc-J3-SI-QH) Kp = 0.0000 kcal/mol, Np =
> 3.0000, Phase = 0.0000 Deg (hc-J3-SI-QS) Kp = 0.2500 kcal/mol, Np
> = 1.0000, Phase = 0.0000 Deg (hc-J3-SI-QS) Kp = 0.0000 kcal/mol,
> Np = 3.0000, Phase = 0.0000 Deg (SI-QS-c3-h1) Kp = 0.3833
> kcal/mol, Np = 3.0000, Phase = 0.0000 Deg (QS-SI-QH-ho) Kp =
> 0.1667 kcal/mol, Np = 3.0000, Phase = 0.0000 Deg (c3-c3-J3-SI) Kp
> = 0.2000 kcal/mol, Np = 1.0000, Phase = 180.0001 Deg (c3-c3-J3-SI)
> Kp = 0.2500 kcal/mol, Np = 2.0000, Phase = 180.0001 Deg
> (c3-c3-J3-SI) Kp = 0.1800 kcal/mol, Np = 3.0000, Phase = 0.0000
> Deg (c3-J3-SI-QH) Kp = 0.1556 kcal/mol, Np = 3.0000, Phase =
> 0.0000 Deg (c3-J3-SI-QS) Kp = 0.1556 kcal/mol, Np = 3.0000, Phase
> = 0.0000 Deg (J3-SI-QS-c3) Kp = 0.1000 kcal/mol, Np = 2.0000,
> Phase = 180.0001 Deg (J3-SI-QS-c3) Kp = 0.3800 kcal/mol, Np =
> 3.0000, Phase = 0.0000 Deg (QH-SI-QS-c3) Kp = 0.3833 kcal/mol, Np
> = 3.0000, Phase = 0.0000 Deg (QS-SI-QS-c3) Kp = 1.3500 kcal/mol,
> Np = 1.0000, Phase = 180.0001 Deg (QS-SI-QS-c3) Kp = 0.8500
> kcal/mol, Np = 2.0000, Phase = 180.0001 Deg (QS-SI-QS-c3) Kp =
> 0.1000 kcal/mol, Np = 3.0000, Phase = 0.0000 Deg
> ------------------------------------------------------------
> -----------------------
> Sum of squares for initial parameters = 639507927287609.5000000000
> kcal^2/mol^2 R^2 value for initial parameters = 0.128447
> Calculated energy with initial parameters for structure 1 = 1755.187168
> KCal/mol Actual energy for structure 1 should be =
> -445806.454765 KCal/mol --------------------------------- SIMPLEX
> MINIMISATION ---------------------------- Minimising function
> SUM_SQUARES_AMBER_STANDARD, using the SIMPLEX METHOD
> -------------------------------------- CONVERGENCE
> -------------------------------- Step 0: Conv= 4.2670E-05
> min=639507927287609.5000,max=639535215666118.6250 avg639521571476864.0000
> Step 1: Conv= 5.7680E-03 min=1226027881.6924 max=1233120095.5567
> avg=1229573988.6245 Step 2: Conv= 0.0000E+00 min=1210774894.5474
> max=1210774894.5474 avg=1210774894.5474
> ------------------------------------------------------------
> -----------------------
> Convergence ratio of 0.0000E+00 is better than convergence criteria
> of 1.0000E-15. Function Converged - Total function evaluations = 107
> 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 = -448515.329474 kcal/mol (hc-c3) Kr
> = 330.6000 kcal/(mol A)^2, r_eq = 1.0969 A (J3-hc) Kr =
> 330.6000 kcal/(mol A)^2, r_eq = 1.0969 A (QH-ho) Kr =
> 371.4000 kcal/(mol A)^2, r_eq = 0.9730 A (c3-h1) Kr =
> 330.6000 kcal/(mol A)^2, r_eq = 1.0969 A (c3-c3) Kr =
> 300.9000 kcal/(mol A)^2, r_eq = 1.5375 A (c3-J3) Kr =
> 300.9000 kcal/(mol A)^2, r_eq = 1.5375 A (J3-SI) Kr =
> 206.0000 kcal/(mol A)^2, r_eq = 1.7800 A (SI-QH) Kr =
> 203.2000 kcal/(mol A)^2, r_eq = 1.7500 A (SI-QS) Kr =
> 599.8000 kcal/(mol A)^2, r_eq = 1.7580 A (QS-c3) Kr =
> 308.6000 kcal/(mol A)^2, r_eq = 1.4316 A (hc-c3-c3) Kt = 46.3400
> kcal/(mol rad)^2, th_eq = 109.8000 deg (hc-c3-hc) Kt = 39.4000
> kcal/(mol rad)^2, th_eq = 107.5800 deg (c3-J3-hc) Kt = 46.3400
> kcal/(mol rad)^2, th_eq = 109.8000 deg (J3-c3-hc) Kt = 46.3400
> kcal/(mol rad)^2, th_eq = 109.8000 deg (hc-J3-SI) Kt = 46.3400
> kcal/(mol rad)^2, th_eq = 109.8000 deg (hc-J3-hc) Kt = 39.4000
> kcal/(mol rad)^2, th_eq = 107.5800 deg (SI-QH-ho) Kt = 47.3800
> kcal/(mol rad)^2, th_eq = 107.2600 deg (QS-c3-h1) Kt = 50.8000
> kcal/(mol rad)^2, th_eq = 109.7800 deg (h1-c3-h1) Kt = 39.2400
> kcal/(mol rad)^2, th_eq = 108.4600 deg (c3-c3-J3) Kt = 62.8600
> kcal/(mol rad)^2, th_eq = 111.5100 deg (c3-J3-SI) Kt = 62.8600
> kcal/(mol rad)^2, th_eq = 111.5100 deg (J3-SI-QH) Kt = 67.4700
> kcal/(mol rad)^2, th_eq = 110.1900 deg (J3-SI-QS) Kt = 68.0000
> kcal/(mol rad)^2, th_eq = 107.9700 deg (SI-QS-c3) Kt = 62.7000
> kcal/(mol rad)^2, th_eq = 112.4800 deg (QH-SI-QS) Kt = 72.5800
> kcal/(mol rad)^2, th_eq = 109.3800 deg (QS-SI-QS) Kt = 72.7400
> kcal/(mol rad)^2, th_eq = 108.2900 deg (hc-c3-c3-J3) Kp = 0.1556
> kcal/mol, Np = 3.0000, Phase = 0.0000 Deg (hc-c3-c3-hc) Kp =
> 0.1500 kcal/mol, Np = 3.0000, Phase = 0.0000 Deg (c3-c3-J3-hc) Kp
> = 0.1600 kcal/mol, Np = 3.0000, Phase = 0.0000 Deg (J3-SI-QH-ho)
> Kp = 0.2500 kcal/mol, Np = 1.0000, Phase = 0.0000 Deg
> (J3-SI-QH-ho) Kp = 0.1600 kcal/mol, Np = 3.0000, Phase = 0.0000
> Deg (hc-c3-J3-hc) Kp = 0.1500 kcal/mol, Np = 3.0000, Phase =
> 0.0000 Deg (hc-c3-J3-SI) Kp = 0.1600 kcal/mol, Np = 3.0000, Phase
> = 0.0000 Deg (hc-J3-SI-QH) Kp = 0.2500 kcal/mol, Np = 1.0000,
> Phase = 0.0000 Deg (hc-J3-SI-QH) Kp = 0.0000 kcal/mol, Np =
> 3.0000, Phase = 0.0000 Deg (hc-J3-SI-QS) Kp = 0.2500 kcal/mol, Np
> = 1.0000, Phase = 0.0000 Deg (hc-J3-SI-QS) Kp = 0.0000 kcal/mol,
> Np = 3.0000, Phase = 0.0000 Deg (SI-QS-c3-h1) Kp = 0.3833
> kcal/mol, Np = 3.0000, Phase = 0.0000 Deg (QS-SI-QH-ho) Kp =
> 0.1667 kcal/mol, Np = 3.0000, Phase = 0.0000 Deg (c3-c3-J3-SI) Kp
> = 0.2000 kcal/mol, Np = 1.0000, Phase = 180.0001 Deg (c3-c3-J3-SI)
> Kp = 0.2500 kcal/mol, Np = 2.0000, Phase = 180.0001 Deg
> (c3-c3-J3-SI) Kp = 0.1800 kcal/mol, Np = 3.0000, Phase = 0.0000
> Deg (c3-J3-SI-QH) Kp = 0.1556 kcal/mol, Np = 3.0000, Phase =
> 0.0000 Deg (c3-J3-SI-QS) Kp = 0.1556 kcal/mol, Np = 3.0000, Phase
> = 0.0000 Deg (J3-SI-QS-c3) Kp = 0.1000 kcal/mol, Np = 2.0000,
> Phase = 180.0001 Deg (J3-SI-QS-c3) Kp = 0.3800 kcal/mol, Np =
> 3.0000, Phase = 0.0000 Deg (QH-SI-QS-c3) Kp = 0.3833 kcal/mol, Np
> = 3.0000, Phase = 0.0000 Deg (QS-SI-QS-c3) Kp = 1.3500 kcal/mol,
> Np = 1.0000, Phase = 180.0001 Deg (QS-SI-QS-c3) Kp = 0.8500
> kcal/mol, Np = 2.0000, Phase = 180.0001 Deg (QS-SI-QS-c3) Kp =
> 0.1000 kcal/mol, Np = 3.0000, Phase = 0.0000 Deg
> ------------------------------------------------------------
> ----------------------|
> Called the fitness function 108 times. Function value with fitted
> parameters = 1210774894.5474, R^2 = 0.1284 Calculated energy with fitted
> parameters for structure 1 = 1755.1872 KCal/mol * Result passed angle
> validity check. * Result passed bond validity check.| Program
> Execution Completed at: Tue Apr 24 16:00:24 2018|
> Elapsed Time = 15.00
> seconds*****************************************************
> *********************************Fitting
> params:
> *****************************************************
> * 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 Apr 24 16:01:56 2018|| Random seed =
> 1524596516 Reading job control file: job_fit.in <http://job_fit.in> Job
> Control: Read a total of 25 lines from job_control file. 19 options set.
> Reading prmtop file : sil.prmtop Prmtop (info): Successfully read
> in saved parameter information Prmtop (unique): Found 10 unique bonds.
> Prmtop (unique): Found 16 unique angles. Prmtop (unique): Found 16
> unique dihedrals. Prmtop (unique): Found 24 unique dihedral terms.
> Reading mdcrd file: sil_valid_structures.mdcrd Reading mdcrd file :
> sil_valid_structures.mdcrd Coordinate file passed format check Reading
> energy file or directory : energy_qm_sil.dat
> ------------------------------------------------------------
> ---------
> | 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 = 10, UNIQUE ANGLES = 16, UNIQUE DIHEDRALS = 16 | |
> NBONDS = 22, NANGLES = 39, NDIHEDRALS = 57 | |
> Total dimensions of fit = 106 | |
> | |
> Sample structures for least squares fit = 3179 |
> | |
> | |
> | Energy Correction Term (K) = -448515.32947400
> | |
> | |
> 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 = 95 bytes |
> | PRMTOP STORAGE = 389242 bytes |
> | COORDINATE STORAGE = 1958304 bytes |
> | GA ARRAY STORAGE = 42400 bytes |
> | |
> | TOTAL ESTIMATED MEMORY USAGE = 2390041 bytes |
> | |
> ------------------------------------------------------------
> ---------
> WARNING: c3-c3-J3-hc dihedral is missing 3 data points in the range
> 2.1991 to 3.1416 radians. WARNING: J3-SI-QH-ho dihedral is missing 6 data
> points in the range 2.1991 to 3.1416 radians. WARNING: hc-c3-J3-hc
> dihedral is missing 3 data points in the range 2.1991 to 3.1416 radians.
> WARNING: hc-c3-J3-SI dihedral is missing 3 data points in the range
> 2.1991 to 3.1416 radians. WARNING: hc-J3-SI-QH dihedral is missing 1 data
> points in the range 2.1991 to 3.1416 radians. WARNING: hc-J3-SI-QS
> dihedral is missing 5 data points in the range 2.1991 to 3.1416 radians.
> WARNING: SI-QS-c3-h1 dihedral is missing 8 data points in the range
> 2.1991 to 3.1416 radians. WARNING: QS-SI-QH-ho dihedral is missing 1 data
> points in the range 2.1991 to 3.1416 radians. WARNING: c3-J3-SI-QH
> dihedral is missing 6 data points in the range 2.1991 to 3.1416 radians.
> WARNING: c3-J3-SI-QS dihedral is missing 1 data points in the range
> 2.1991 to 3.1416 radians. WARNING: QH-SI-QS-c3 dihedral is missing 3 data
> points in the range 2.1991 to 3.1416 radians. WARNING: QS-SI-QS-c3
> dihedral is missing 3 data points in the range 2.1991 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 = -448515.329474 kcal/mol (hc-c3) Kr
> = 330.6000 kcal/(mol A)^2, r_eq = 1.0969 A (J3-hc)*Kr =
> 330.6000 kcal/(mol A)^2,*r_eq = 1.0969 A (QH-ho)*Kr =
> 371.4000 kcal/(mol A)^2,*r_eq = 0.9730 A (c3-h1) Kr =
> 330.6000 kcal/(mol A)^2, r_eq = 1.0969 A (c3-c3) Kr =
> 300.9000 kcal/(mol A)^2, r_eq = 1.5375 A (c3-J3)*Kr =
> 300.9000 kcal/(mol A)^2,*r_eq = 1.5375 A (J3-SI)*Kr =
> 206.0000 kcal/(mol A)^2,*r_eq = 1.7800 A (SI-QH)*Kr =
> 203.2000 kcal/(mol A)^2,*r_eq = 1.7500 A (SI-QS)*Kr =
> 599.8000 kcal/(mol A)^2,*r_eq = 1.7580 A (QS-c3)*Kr =
> 308.6000 kcal/(mol A)^2,*r_eq = 1.4316 A (hc-c3-c3) Kt = 46.3400
> kcal/(mol rad)^2, th_eq = 109.8000 deg (hc-c3-hc) Kt = 39.4000
> kcal/(mol rad)^2, th_eq = 107.5800 deg (c3-J3-hc)*Kt = 46.3400
> kcal/(mol rad)^2, *th_eq = 109.8000 deg (J3-c3-hc)*Kt = 46.3400
> kcal/(mol rad)^2, *th_eq = 109.8000 deg (hc-J3-SI)*Kt = 46.3400
> kcal/(mol rad)^2, *th_eq = 109.8000 deg (hc-J3-hc)*Kt = 39.4000
> kcal/(mol rad)^2, *th_eq = 107.5800 deg (SI-QH-ho)*Kt = 47.3800
> kcal/(mol rad)^2, *th_eq = 107.2600 deg (QS-c3-h1)*Kt = 50.8000
> kcal/(mol rad)^2, *th_eq = 109.7800 deg (h1-c3-h1) Kt = 39.2400
> kcal/(mol rad)^2, th_eq = 108.4600 deg (c3-c3-J3)*Kt = 62.8600
> kcal/(mol rad)^2, *th_eq = 111.5100 deg (c3-J3-SI)*Kt = 62.8600
> kcal/(mol rad)^2, *th_eq = 111.5100 deg (J3-SI-QH)*Kt = 67.4700
> kcal/(mol rad)^2, *th_eq = 110.1900 deg (J3-SI-QS)*Kt = 68.0000
> kcal/(mol rad)^2, *th_eq = 107.9700 deg (SI-QS-c3)*Kt = 62.7000
> kcal/(mol rad)^2, *th_eq = 112.4800 deg (QH-SI-QS)*Kt = 72.5800
> kcal/(mol rad)^2, *th_eq = 109.3800 deg (QS-SI-QS)*Kt = 72.7400
> kcal/(mol rad)^2, *th_eq = 108.2900 deg (hc-c3-c3-J3) Kp = 0.1556
> kcal/mol, Np = 3.0000, Phase = 0.0000 Deg (hc-c3-c3-hc) Kp =
> 0.1500 kcal/mol, Np = 3.0000, Phase = 0.0000 Deg (c3-c3-J3-hc)*Kp
> = 0.1600 kcal/mol, *Np = 3.0000, *Phase = 0.0000 Deg
> (J3-SI-QH-ho)*Kp = 0.2500 kcal/mol, *Np = 1.0000, *Phase = 0.0000
> Deg (J3-SI-QH-ho)*Kp = 0.1600 kcal/mol, *Np = 3.0000, *Phase =
> 0.0000 Deg (hc-c3-J3-hc)*Kp = 0.1500 kcal/mol, *Np = 3.0000,
> *Phase = 0.0000 Deg (hc-c3-J3-SI)*Kp = 0.1600 kcal/mol, *Np =
> 3.0000, *Phase = 0.0000 Deg (hc-J3-SI-QH)*Kp = 0.2500 kcal/mol,
> *Np = 1.0000, *Phase = 0.0000 Deg (hc-J3-SI-QH)*Kp = 0.0000
> kcal/mol, *Np = 3.0000, *Phase = 0.0000 Deg (hc-J3-SI-QS)*Kp =
> 0.2500 kcal/mol, *Np = 1.0000, *Phase = 0.0000 Deg
> (hc-J3-SI-QS)*Kp = 0.0000 kcal/mol, *Np = 3.0000, *Phase = 0.0000
> Deg (SI-QS-c3-h1)*Kp = 0.3833 kcal/mol, *Np = 3.0000, *Phase =
> 0.0000 Deg (QS-SI-QH-ho)*Kp = 0.1667 kcal/mol, *Np = 3.0000,
> *Phase = 0.0000 Deg (c3-c3-J3-SI)*Kp = 0.2000 kcal/mol, *Np =
> 1.0000, *Phase = 180.0001 Deg (c3-c3-J3-SI)*Kp = 0.2500 kcal/mol,
> *Np = 2.0000, *Phase = 180.0001 Deg (c3-c3-J3-SI)*Kp = 0.1800
> kcal/mol, *Np = 3.0000, *Phase = 0.0000 Deg (c3-J3-SI-QH)*Kp =
> 0.1556 kcal/mol, *Np = 3.0000, *Phase = 0.0000 Deg
> (c3-J3-SI-QS)*Kp = 0.1556 kcal/mol, *Np = 3.0000, *Phase = 0.0000
> Deg (J3-SI-QS-c3)*Kp = 0.1000 kcal/mol, *Np = 2.0000, *Phase =
> 180.0001 Deg (J3-SI-QS-c3)*Kp = 0.3800 kcal/mol, *Np = 3.0000,
> *Phase = 0.0000 Deg (QH-SI-QS-c3)*Kp = 0.3833 kcal/mol, *Np =
> 3.0000, *Phase = 0.0000 Deg (QS-SI-QS-c3)*Kp = 1.3500 kcal/mol,
> *Np = 1.0000, *Phase = 180.0001 Deg (QS-SI-QS-c3)*Kp = 0.8500
> kcal/mol, *Np = 2.0000, *Phase = 180.0001 Deg (QS-SI-QS-c3)*Kp =
> 0.1000 kcal/mol, *Np = 3.0000, *Phase = 0.0000 Deg
> ------------------------------------------------------------
> -----------------------
> Sum of squares for initial parameters = 1210774894.5474364758
> kcal^2/mol^2 R^2 value for initial parameters = 0.128447
> Calculated energy with initial parameters for structure 1 =
> -446760.142306 KCal/mol Actual energy for structure 1 should be
> = -445806.454765 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=
> 18647979251.09495 Mean= 9.4959e+10 Elapsed= 0/3 Gen 1: Best=
> 6560889700.15635 Mean= 3.104e+10 Elapsed= 1/3 Gen 2: Best=
> 6037927240.01578 Mean= 1.4724e+10 Elapsed= 2/3 Gen 3: Best=
> 1786601688.49046 Mean= 7.1246e+09 Conv= 0/20 Gen 4: Best=
> 1693572720.87644 Mean= 3.511e+09 Conv= 0/20 Gen 5: Best=
> 1147401350.81570 Mean= 2.377e+09 Conv= 0/20 Gen 6: Best=
> 765972354.13971 Mean= 1.6021e+09 Conv= 0/20 Gen 7: Best=
> 643182819.48873 Mean= 1.1472e+09 Conv= 0/20 Gen 8: Best=
> 534346254.81285 Mean= 9.1876e+08 Conv= 0/20 Gen 9: Best=
> 451637044.04493 Mean= 7.3701e+08 Conv= 0/20 Gen 10: Best=
> 409141148.15124 Mean= 6.2672e+08 Conv= 0/20 Gen 11: Best=
> 409141148.15124 Mean= 5.5956e+08 Conv= 1/20 Gen 12: Best=
> 406983149.33790 Mean= 5.0769e+08 Conv= 0/20 Gen 13: Best=
> 406983149.33790 Mean= 4.6599e+08 Conv= 1/20 Gen 14: Best=
> 398136217.24745 Mean= 4.6672e+08 Conv= 0/20 Gen 15: Best=
> 398136217.24745 Mean= 4.6499e+08 Conv= 1/20 Gen 16: Best=
> 395144588.46458 Mean= 4.6438e+08 Conv= 0/20 Gen 17: Best=
> 395144588.46458 Mean= 4.7961e+08 Conv= 1/20 Gen 18: Best=
> 393492147.90650 Mean= 4.9342e+08 Conv= 0/20 Gen 19: Best=
> 391401224.74145 Mean= 4.4268e+08 Conv= 0/20 Gen 20: Best=
> 382821607.46150 Mean= 4.1161e+08 Conv= 0/20 Gen 21: Best=
> 382821607.46150 Mean= 4.3017e+08 Conv= 1/20 Gen 22: Best=
> 382821607.46150 Mean= 4.4077e+08 Conv= 2/20 Gen 23: Best=
> 382196737.69895 Mean= 4.429e+08 Conv= 0/20 Gen 24: Best=
> 380481264.94396 Mean= 4.3291e+08 Conv= 0/20 Gen 25: Best=
> 376365560.03290 Mean= 4.3582e+08 Conv= 0/20 Gen 26: Best=
> 376365560.03290 Mean= 4.5119e+08 Conv= 1/20 Gen 27: Best=
> 375981189.52794 Mean= 4.0561e+08 Conv= 0/20 Gen 28: Best=
> 372604200.94957 Mean= 4.3649e+08 Conv= 0/20 Gen 29: Best=
> 372604200.94957 Mean= 4.1719e+08 Conv= 1/20 Gen 30: Best=
> 372604200.94957 Mean= 4.1013e+08 Conv= 2/20 Gen 31: Best=
> 371351456.91688 Mean= 4.2437e+08 Conv= 0/20 Gen 32: Best=
> 370164769.69229 Mean= 3.9231e+08 Conv= 0/20 Gen 33: Best=
> 370164769.69229 Mean= 3.9507e+08 Conv= 1/20 Gen 34: Best=
> 367736163.62116 Mean= 3.9787e+08 Conv= 0/20 Gen 35: Best=
> 366257712.21955 Mean= 4.0259e+08 Conv= 0/20 Gen 36: Best=
> 364528801.95150 Mean= 4.1774e+08 Conv= 0/20 Gen 37: Best=
> 363776664.50556 Mean= 4.0479e+08 Conv= 0/20 Gen 38: Best=
> 363776664.50556 Mean= 3.8876e+08 Conv= 1/20 Gen 39: Best=
> 363491609.83458 Mean= 4.018e+08 Conv= 0/20 Gen 40: Best=
> 363491609.83458 Mean= 4.155e+08 Conv= 1/20 Gen 41: Best=
> 361784759.74303 Mean= 3.9343e+08 Conv= 0/20 Gen 42: Best=
> 361689243.86095 Mean= 4.2228e+08 Conv= 0/20 Gen 43: Best=
> 361689243.86095 Mean= 4.0025e+08 Conv= 1/20 Gen 44: Best=
> 360291863.15822 Mean= 3.829e+08 Conv= 0/20 Gen 45: Best=
> 359652679.24202 Mean= 3.8505e+08 Conv= 0/20 Gen 46: Best=
> 359652679.24202 Mean= 3.8183e+08 Conv= 1/20 Gen 47: Best=
> 359652679.24202 Mean= 4.3711e+08 Conv= 2/20 Gen 48: Best=
> 359652679.24202 Mean= 3.7199e+08 Conv= 3/20 Gen 49: Best=
> 358924315.80432 Mean= 4.1739e+08 Conv= 0/20 Gen 50: Best=
> 358924315.80432 Mean= 3.8507e+08 Conv= 1/20 Gen 51: Best=
> 357363696.46246 Mean= 4.0406e+08 Conv= 0/20 Gen 52: Best=
> 356748803.40086 Mean= 3.891e+08 Conv= 0/20 Gen 53: Best=
> 356748803.40086 Mean= 4.0941e+08 Conv= 1/20 Gen 54: Best=
> 356722621.62196 Mean= 3.9548e+08 Conv= 0/20 Gen 55: Best=
> 355264563.40011 Mean= 3.9173e+08 Conv= 0/20 Gen 56: Best=
> 355264563.40011 Mean= 3.8777e+08 Conv= 1/20 Gen 57: Best=
> 354345615.64727 Mean= 4.0617e+08 Conv= 0/20 Gen 58: Best=
> 354345615.64727 Mean= 3.8516e+08 Conv= 1/20 Gen 59: Best=
> 354345615.64727 Mean= 3.6743e+08 Conv= 2/20 Gen 60: Best=
> 354303310.32536 Mean= 3.7875e+08 Conv= 0/20 Gen 61: Best=
> 354303310.32536 Mean= 3.7385e+08 Conv= 1/20 Gen 62: Best=
> 354303310.32536 Mean= 4.0586e+08 Conv= 2/20 Gen 63: Best=
> 354042568.20568 Mean= 3.6868e+08 Conv= 0/20 Gen 64: Best=
> 354042568.20568 Mean= 3.705e+08 Conv= 1/20 Gen 65: Best=
> 353809227.80321 Mean= 3.8219e+08 Conv= 0/20 Gen 66: Best=
> 352781401.63759 Mean= 3.7582e+08 Conv= 0/20 Gen 67: Best=
> 352781401.63759 Mean= 4.2363e+08 Conv= 1/20 Gen 68: Best=
> 352781401.63759 Mean= 3.6696e+08 Conv= 2/20 Gen 69: Best=
> 352676170.07200 Mean= 3.8707e+08 Conv= 0/20 Gen 70: Best=
> 352234543.73541 Mean= 3.7087e+08 Conv= 0/20 Gen 71: Best=
> 350994595.38598 Mean= 3.7909e+08 Conv= 0/20 Gen 72: Best=
> 350994595.38598 Mean= 3.7469e+08 Conv= 1/20 Gen 73: Best=
> 350994595.38598 Mean= 3.7942e+08 Conv= 2/20 Gen 74: Best=
> 350451685.81318 Mean= 3.6566e+08 Conv= 0/20 Gen 75: Best=
> 350451685.81318 Mean= 3.7723e+08 Conv= 1/20 Gen 76: Best=
> 350007069.83132 Mean= 3.7054e+08 Conv= 0/20 Gen 77: Best=
> 350007069.83132 Mean= 4.0709e+08 Conv= 1/20 Gen 78: Best=
> 350007069.83132 Mean= 3.6684e+08 Conv= 2/20 Gen 79: Best=
> 350007069.83132 Mean= 3.758e+08 Conv= 3/20 Gen 80: Best=
> 350007069.83132 Mean= 3.7091e+08 Conv= 4/20 Gen 81: Best=
> 349899368.43892 Mean= 3.6691e+08 Conv= 0/20 Gen 82: Best=
> 349148157.40629 Mean= 3.9073e+08 Conv= 0/20 Gen 83: Best=
> 349148157.40629 Mean= 3.8346e+08 Conv= 1/20 Gen 84: Best=
> 349148157.40629 Mean= 3.6386e+08 Conv= 2/20 Gen 85: Best=
> 349148157.40629 Mean= 3.6123e+08 Conv= 3/20 Gen 86: Best=
> 349148157.40629 Mean= 3.6657e+08 Conv= 4/20 Gen 87: Best=
> 349148157.40629 Mean= 3.8482e+08 Conv= 5/20 Gen 88: Best=
> 340673858.23786 Mean= 3.5652e+08 Conv= 0/20 Gen 89: Best=
> 340673858.23786 Mean= 3.6666e+08 Conv= 1/20 Gen 90: Best=
> 340673858.23786 Mean= 3.8797e+08 Conv= 2/20 Gen 91: Best=
> 340673858.23786 Mean= 3.7432e+08 Conv= 3/20 Gen 92: Best=
> 340673858.23786 Mean= 3.9087e+08 Conv= 4/20 Gen 93: Best=
> 340673858.23786 Mean= 3.704e+08 Conv= 5/20 Gen 94: Best=
> 340673858.23786 Mean= 3.8692e+08 Conv= 6/20 Gen 95: Best=
> 340673858.23786 Mean= 4.2573e+08 Conv= 7/20 Gen 96: Best=
> 340673858.23786 Mean= 4.0786e+08 Conv= 8/20 Gen 97: Best=
> 340673858.23786 Mean= 3.9192e+08 Conv= 9/20 Gen 98: Best=
> 340673858.23786 Mean= 4.1079e+08 Conv= 10/20 Gen 99: Best=
> 340673858.23786 Mean= 4.054e+08 Conv= 11/20 Gen 100: Best=
> 340673858.23786 Mean= 3.9812e+08 Conv= 12/20 Gen 101: Best=
> 340673858.23786 Mean= 4.0434e+08 Conv= 13/20 Gen 102: Best=
> 340673858.23786 Mean= 3.8863e+08 Conv= 14/20 Gen 103: Best=
> 340673858.23786 Mean= 4.3084e+08 Conv= 15/20 Gen 104: Best=
> 340673858.23786 Mean= 3.8888e+08 Conv= 16/20 Gen 105: Best=
> 340673858.23786 Mean= 4.2465e+08 Conv= 17/20 Gen 106: Best=
> 340673858.23786 Mean= 4.0347e+08 Conv= 18/20 Gen 107: Best=
> 340673858.23786 Mean= 4.1714e+08 Conv= 19/20 Gen 108: Best=
> 340673858.23786 Mean= 4.2757e+08 Conv= 20/20| Took 109
> generations to converge. ------------------------------- FINAL
> PARAMETERS
> --------------------------------- Parameters for force field equation:
> AMBER_STANDARD: (* means parameter is NOT constant during fit)
> K = -448515.329474 kcal/mol (hc-c3) Kr
> = 330.6000 kcal/(mol A)^2, r_eq = 1.0969 A (J3-hc)*Kr =
> 472.5250 kcal/(mol A)^2,*r_eq = 1.4158 A (QH-ho)*Kr =
> 594.0627 kcal/(mol A)^2,*r_eq = 1.9971 A (c3-h1) Kr =
> 330.6000 kcal/(mol A)^2, r_eq = 1.0969 A (c3-c3) Kr =
> 300.9000 kcal/(mol A)^2, r_eq = 1.5375 A (c3-J3)*Kr =
> 151.8351 kcal/(mol A)^2,*r_eq = 1.7015 A (J3-SI)*Kr =
> 390.5055 kcal/(mol A)^2,*r_eq = 2.0791 A (SI-QH)*Kr =
> 305.0406 kcal/(mol A)^2,*r_eq = 1.8434 A (SI-QS)*Kr =
> 325.4793 kcal/(mol A)^2,*r_eq = 1.6804 A (QS-c3)*Kr =
> 174.5176 kcal/(mol A)^2,*r_eq = 1.2920 A (hc-c3-c3) Kt = 46.3400
> kcal/(mol rad)^2, th_eq = 109.8000 deg (hc-c3-hc) Kt = 39.4000
> kcal/(mol rad)^2, th_eq = 107.5800 deg (c3-J3-hc)*Kt = 49.9651
> kcal/(mol rad)^2, *th_eq = 106.7322 deg (J3-c3-hc)*Kt = 63.6053
> kcal/(mol rad)^2, *th_eq = 118.8835 deg (hc-J3-SI)*Kt = 31.5124
> kcal/(mol rad)^2, *th_eq = 42.6351 deg (hc-J3-hc)*Kt = 68.5580
> kcal/(mol rad)^2, *th_eq = 69.9189 deg (SI-QH-ho)*Kt = 63.9186
> kcal/(mol rad)^2, *th_eq = 96.8686 deg (QS-c3-h1)*Kt = 22.5033
> kcal/(mol rad)^2, *th_eq = 90.5631 deg (h1-c3-h1) Kt = 39.2400
> kcal/(mol rad)^2, th_eq = 108.4600 deg (c3-c3-J3)*Kt = 81.1675
> kcal/(mol rad)^2, *th_eq = 102.9205 deg (c3-J3-SI)*Kt = 105.9694
> kcal/(mol rad)^2, *th_eq = 106.0494 deg (J3-SI-QH)*Kt = 65.1868
> kcal/(mol rad)^2, *th_eq = 108.4246 deg (J3-SI-QS)*Kt = 111.4691
> kcal/(mol rad)^2, *th_eq = 105.0050 deg (SI-QS-c3)*Kt = 38.3763
> kcal/(mol rad)^2, *th_eq = 131.9844 deg (QH-SI-QS)*Kt = 72.6304
> kcal/(mol rad)^2, *th_eq = 96.7934 deg (QS-SI-QS)*Kt = 50.2373
> kcal/(mol rad)^2, *th_eq = 126.1219 deg (hc-c3-c3-J3) Kp = 0.1556
> kcal/mol, Np = 3.0000, Phase = 0.0000 Deg (hc-c3-c3-hc) Kp =
> 0.1500 kcal/mol, Np = 3.0000, Phase = 0.0000 Deg (c3-c3-J3-hc)*Kp
> = 6.4750 kcal/mol, *Np = 26.6783, *Phase = -6.1278 Deg
> (J3-SI-QH-ho)*Kp = 9.7732 kcal/mol, *Np = 3.6921, *Phase = 207.2873
> Deg (J3-SI-QH-ho)*Kp = -3.0303 kcal/mol, *Np = 1.7098, *Phase =
> 278.4416 Deg (hc-c3-J3-hc)*Kp = 2.8210 kcal/mol, *Np = 1.9920,
> *Phase = 133.5388 Deg (hc-c3-J3-SI)*Kp = 21.0019 kcal/mol, *Np =
> 1.2447, *Phase = 99.3623 Deg (hc-J3-SI-QH)*Kp = -12.3814 kcal/mol,
> *Np = -1.0410, *Phase = 26.6607 Deg (hc-J3-SI-QH)*Kp = 20.4284
> kcal/mol, *Np = 1.3169, *Phase = 201.8146 Deg (hc-J3-SI-QS)*Kp =
> 8.5730 kcal/mol, *Np = -0.6379, *Phase = 39.2938 Deg
> (hc-J3-SI-QS)*Kp = 11.8003 kcal/mol, *Np = 2.4998, *Phase = 88.4351
> Deg (SI-QS-c3-h1)*Kp = -25.5281 kcal/mol, *Np = 0.0243, *Phase =
> -24.8028 Deg (QS-SI-QH-ho)*Kp = 21.8104 kcal/mol, *Np = 3.2271,
> *Phase = 118.7320 Deg (c3-c3-J3-SI)*Kp = 20.0965 kcal/mol, *Np =
> 1.3988, *Phase = 234.6185 Deg (c3-c3-J3-SI)*Kp = 12.0612 kcal/mol,
> *Np = 2.6108, *Phase = 99.6986 Deg (c3-c3-J3-SI)*Kp = 9.8252
> kcal/mol, *Np = 3.0325, *Phase = 205.0968 Deg (c3-J3-SI-QH)*Kp =
> 20.5404 kcal/mol, *Np = 17.1251, *Phase = 118.2318 Deg
> (c3-J3-SI-QS)*Kp = 8.9649 kcal/mol, *Np = 9.0890, *Phase = 106.1252
> Deg (J3-SI-QS-c3)*Kp = 10.5819 kcal/mol, *Np = 4.5773, *Phase =
> 96.1051 Deg (J3-SI-QS-c3)*Kp = 8.4764 kcal/mol, *Np = 13.8000,
> *Phase = 142.5969 Deg (QH-SI-QS-c3)*Kp = 13.0143 kcal/mol, *Np =
> 10.1420, *Phase = 124.4277 Deg (QS-SI-QS-c3)*Kp = -7.0472 kcal/mol,
> *Np = 0.3521, *Phase = 50.3114 Deg (QS-SI-QS-c3)*Kp = 1.5285
> kcal/mol, *Np = -0.2004, *Phase = 99.3010 Deg (QS-SI-QS-c3)*Kp =
> -4.8754 kcal/mol, *Np = -4.0552, *Phase = 77.7451 Deg
> ------------------------------------------------------------
> ----------------------|
> Called the fitness function 33944 times. Function value with fitted
> parameters = 340673858.2379, R^2 = 0.6648 Calculated energy with fitted
> parameters for structure 1 = 2727.9092 KCal/mol * Saving energy file with
> 3179 structures to fit_output_energy.dat WARNING: J3-c3-hc angle has no
> sample structures after it, nearest sample is 0.2634 radians before.
> WARNING: hc-J3-hc angle has no sample structures before it, nearest
> sample is 0.0717 radians after. WARNING: J3-SI-QS angle has no sample
> structures before it, nearest sample is 0.0199 radians after. WARNING:
> SI-QS-c3 angle has no sample structures after it, nearest sample is 0.0810
> radians before. WARNING: QS-SI-QS angle has no sample structures after
> it, nearest sample is 0.2308 radians before. WARNING: Insufficient angle
> information in sample structures. Your settings require that
> sample data exist within 0.157 radians of the algorithm's
> result. Either 1) Add the missing input data
> or 2) Set ANGLE_LIMIT to a larger value
> or 3) Set BOUNDS_CHECK to warn (not
> recommended). Please read the help and/or documentation.
> WARNING: J3-hc bond has no sample structures larger than it,
> nearest sample is 0.3159 A smaller. WARNING: SI-QS bond has no sample
> structures larger than it, nearest sample is 0.0326 A smaller. WARNING:
> Insufficient bond information in sample structures. Your
> settings require that sample data exist within 0.100 A of
> the algorithm's result. Either 1) Add the
> missing input data or 2) Set BOND_LIMIT
> to a larger value or 3) Set BOUNDS_CHECK to
> warn (not recommended). Please read the help and/or
> documentation. | Program Execution Completed at:
> Tue Apr 24 17:14:12 2018| Elapsed Time = 4336.00
> seconds*****************************************************
> ********************************--
> *
> Alechania Misturini
> Mestranda em Físico-Química
> Bacharel e Licenciada em Química
> Grupo de Estrutura Eletrônica Molecular –〈
> GE
> ⎜
> EM
> 〉
> *Departamento de Química – CFM*
> *Universidade Federal de Santa Catarina – UFSC*
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>
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Received on Fri Apr 27 2018 - 08:00:02 PDT
