Ammm:Lig ion params
Introduction
Parameters in AMOEBA
- Water first being parameterized
- ions, organic molecules, proteins and nucleic acids (under improvement)
How to get parameters
- Experiment
- Ab initio QM
- Other force field
Unique parameters in AMOEBA
- Multipole (up to quadrupole)
- Polarizability
- Damping factor
Electrostatic Parameters of AMOEBA
Metal Ion Parameterization
Why model metal ions?
Ions play important roles in biological function
Nearly half of all proteins contain metal ions
- Ion channel (Na+/K+)
- Protein biosynthesis (Mg2+)
- Coagulation cascade (Ca2+)
- Pathogenesis of viruses (Zn2+)
What are the challenges
- High charge density
- Strong polarization effect
- Charge transfer effect
- Can’t be explained by coulumb’s law. Quantum effect.
- Split orbital
- Transition metal, e.g. Zn++
Polarizable vs non-polarizable force field in ion modeling
- Both polarizable and nonpolarizable force fields handle monovalent ions reasonably.
- In case of divalent ions, polarizable force fields give much better result. [1].
Above figures adapted from Warshel et al. JCTC 2007.
Parameterization
What parameters are needed?
- Bonded parameters (bond, angle, torsion and out-of-plane)
- Non-bonded parameters
- Van der Waals
- Electrostatics
How to parameterize
- Charge is known (2+)
- Dipole and quadrupole are 0
- Polarizability determined from B3LYP/6-31G* calculation
- Van der Waals and damping factor (R,ε,a) are determined by fitting to QM dimer energy
- Optimize (Cation-water) dimer structure with B3LYP/6-31G*
- Vary the separation between cation and water molecule with fixed optimized geometry.
- Compute the binding energy versus separation with both QM and AMOEBA. Binding energy = total energy - isolated energy of ion - isolated energy of water
- Tune the parameters to get the best fit.
HF: Hartree-Fock method is an approximate method for the determination of the ground-state wave function, sometimes called SCF (self-consistent field)
MP2: Møller–Plesset theory is based on HF method. It improves on the Hartree–Fock method by adding electron correlation effects to the second order. Mp3 (third), MP4 (fourth).
B3LYP: Hybrid functional. Approximation to density functional theory that incorporates a portion of exact exchange from Hartree-Fock theory with exchange and correlation from other sources (ab initio or empirical)
Case study
Example of gaussian input file for polarizability calculation
%Mem=800MB %Chk=polar.chk #B3LYP/6-311++G(2d,2p) SP Polar MaxDisk=10GB sp energy 2,1 Ca1 0.871756 -0.000003 0.000002
Output file
....skipping...
Electronic spatial extent (au): <R**2>= 15.4404
Charge= 2.0000 electrons
Dipole moment (field-independent basis, Debye):
X= 0.0000 Y= 0.0000 Z= 0.0000 Tot= 0.0000
Quadrupole moment (field-independent basis, Debye-Ang):
XX= -6.9226 YY= -6.9226 ZZ= -6.9226
XY= 0.0000 XZ= 0.0000 YZ= 0.0000
Traceless Quadrupole moment (field-independent basis, Debye-Ang):
XX= 0.0000 YY= 0.0000 ZZ= 0.0000
XY= 0.0000 XZ= 0.0000 YZ= 0.0000
Octapole moment (field-independent basis, Debye-Ang**2):
XXX= 0.0000 YYY= 0.0000 ZZZ= 0.0000 XYY= 0.0000
XXY= 0.0000 XXZ= 0.0000 XZZ= 0.0000 YZZ= 0.0000
YYZ= 0.0000 XYZ= 0.0000
Hexadecapole moment (field-independent basis, Debye-Ang**3):
XXXX= -3.3848 YYYY= -3.3848 ZZZZ= -3.3848 XXXY= 0.0000
XXXZ= 0.0000 YYYX= 0.0000 YYYZ= 0.0000 ZZZX= 0.0000
ZZZY= 0.0000 XXYY= -1.1283 XXZZ= -1.1283 YYZZ= -1.1283
XXYZ= 0.0000 YYXZ= 0.0000 ZZXY= 0.0000
N-N= 0.000000000000D+00 E-N=-1.591920174717D+03 KE= 6.759685000409D+02
Symmetry AG KE= 4.581170345941D+02
Symmetry B1G KE= 2.744378782701D-61
Symmetry B2G KE= 2.109222553139D-61
Symmetry B3G KE= 3.141249198819D-61
Symmetry AU KE= 0.000000000000D+00
Symmetry B1U KE= 7.261715514895D+01
Symmetry B2U KE= 7.261715514895D+01
Symmetry B3U KE= 7.261715514895D+01
Exact polarizability: 3.216 0.000 3.216 0.000 0.000 3.216
Approx polarizability: 4.622 0.000 4.622 0.000 0.000 4.622
1\1\GINC-NODE12\SP\RB3LYP\6-311++G(2d,2p)\Ca1(2+)\OSCAR\05-Jan-2006\0\
\#B3LYP/6-311++G(2D,2P) SP POLAR MAXDISK=10GB\\sp energy\\2,1\Ca,0,0.8
71756,-0.000003,0.000002\\Version=IA32L-G03RevC.02\State=1-A1G\HF=-676
.9057847\RMSD=6.491e-10\Dipole=0.,0.,0.\Polar=3.2162085,0.,3.2162085,0
....skipping...
Bohr Radius = 0.529 177 2083 Å
Basis set superposition error (BSSE). In quantum chemistry, calculations of interaction energies are susceptible to BSSE. As two molecules approach one another, their basis functions overlap. Counterpoise method to eliminate the error. To define basis set internally, use the keyword Gen.
Input file of Gaussian energy calculation
#MP2/Gen SP counterpoise=2 MaxDisk=10GB
sp energy
2,1,2,1,0,1
Ca1 -0.628244 -0.000003 0.000002 1
O2 1.471756 -0.000020 -0.000018 2
H3 2.069508 -0.764665 0.000058 2
H4 2.069178 0.764883 0.000058 2
CA 0
S 19 1.00
7503960.00 0.224000000E-05
1123486.00 0.174400000E-04
....skipping....
P 1 1.00
0.144000000 1.00000000
P 1 1.00
0.580000000E-01 1.00000000
P 1 1.00
0.231600000E-01 1.00000000
D 4 1.00
26.2708300 0.734600000E-02
7.30782000 0.409010000E-01
2.45498000 0.130065000
0.887140000 0.244151000
D 1 1.00
0.309250000 1.00000000
D 1 1.00
0.103160000 1.00000000
D 1 1.00
0.337400000E-01 1.00000000
F 1 1.00
0.488300000 1.00000000
F 1 1.00
0.116500000 1.00000000
G 1 1.00
0.146600000 1.00000000
****
H O 0
cc-pvqz
****
Output
Hexadecapole moment (field-independent basis, Debye-Ang**3): XXXX= -20.3681 YYYY= -5.8454 ZZZZ= -6.0461 XXXY= -0.0019 XXXZ= 0.0006 YYYX= 0.0008 YYYZ= 0.0000 ZZZX= 0.0001 ZZZY= 0.0000 XXYY= -1.9087 XXZZ= -5.9481 YYZZ= -2.3208 XXYZ= 0.0000 YYXZ= 0.0002 ZZXY= 0.0000 N-N= 9.069616433324D+00 E-N=-1.988243128533D+02 KE= 7.595642684817D+01 Counterpoise: corrected energy = -750.764481575760 Counterpoise: BSSE energy = 0.003336990775 1\1\GINC-NODE5\SP\RMP2-FC\Gen\Ca1H2O1(2+)\OSCAR\29-Dec-2005\0\\#MP2/GE N SP COUNTERPOISE=2 MAXDISK=10GB\\sp energy\\2,1\Ca,0,0.471756,-0.0000 03,0.000002\O,0,1.471756,-0.00002,-0.000018\H,0,2.069508,-0.764665,0.0 00058\H,0,2.069178,0.764883,0.000058\\Version=IA32L-G03RevC.02\State=1 -A\HF=-76.0635232\MP2=-76.3473292\RMSD=2.782e-09\PG=C01 [X(Ca1H2O1)]\\ @
1 Hartree = 627.509 kcal/mol
TINKER input (xyz)
4 Ca-wat
1 Ca+ -0.628244 -0.000003 0.000002 18
2 O 1.471756 -0.000020 -0.000018 61 3 4
3 H 2.069508 -0.764665 0.000058 62 2
4 H 2.069178 0.764883 0.000058 62 2
TINKER output (command analyze)
Total Potential Energy : -10.9037 Kcal/mole Intermolecular Energy : -11.3330 Kcal/mole Energy Component Breakdown : Kcal/mole Interactions Bond Stretching 0.1828 2 Angle Bending 0.2243 1 Urey-Bradley 0.0223 1 Van der Waals -0.0492 3 Atomic Multipoles -10.0915 3 Polarization -1.1923 3
Small ligand parameterization
Build your ligand
(1) Make your molecule with Chem3D Ultra or Arguslab (windows)
(2) Minimize the structure. Once the molecule is built, minimize energy with any of the methods available in Chem3D. There are other ways to minimize energy: MOPAC, MM2, Gaussian, Mechanics. You can use any of them as long as it works.
(3) Save the structure as xyz file.
Save as Tinker MM3 Input (*.xyz), benz.xyz
Optimize structure with QM
(1) Convert .xyz to .com
Just copy the atoms and their coordinates into the .com file with following format:
%chk=benz.chk %mem=50MW %nproc=2 # opt hf/6-31g* opt energy 1 1 C 0.310792 0.313000 -0.224530 C -0.125208 0.944000 0.941470 C -0.473208 0.250000 2.081470 C -0.397208 -1.110000 2.090470 C 0.025792 -1.764000 0.961470 C 0.376792 -1.071000 -0.177530 C 0.655792 1.023000 -1.380530 N 1.378792 0.421000 -2.305530 N 0.251792 2.268000 -1.515530 N -0.666208 -1.665000 2.975470 H -0.197208 2.021000 0.966470 H -0.807208 0.776000 2.964470 H 0.078792 -2.841000 0.960470 H 0.706792 -1.627000 -1.043530 H 1.626117 -0.505205 -1.989348 H 1.663792 0.848000 -3.156530 H -0.246151 2.554668 -0.678924 H 0.471792 2.841000 -2.290530 H -0.548431 -2.662838 2.799895 H -1.663792 -1.553551 3.156530 <blank line>
(2) Run Gaussian program to optimize the structure.
Single Point calculation
(1) Make the single point file (.com)
Extract the optimized coordinates from opt output file (.log) and set up a single point calculation
%Mem=500MB %Nosave %Chk=benzsp.chk %Nproc=2 #MP2/6-311++G(2d,2p) Sp Density=MP2 MaxDisk=960MW sp energy 1 1 C1 0.293566 0.297615 -0.240256 C2 -0.088764 0.943618 0.941596 C3 -0.462820 0.230827 2.043653 C4 -0.490542 -1.177405 2.018026 C5 -0.112718 -1.822504 0.824061 C6 0.275038 -1.102026 -0.268251 C7 0.697450 1.057005 -1.402781 N8 1.606270 0.574513 -2.231120 N9 0.160802 2.239323 -1.645792 N10 -0.865410 -1.882805 3.098002 H11 -0.050701 2.013222 1.010215 H12 -0.729196 0.743799 2.944741 H13 -0.141810 -2.891482 0.774237 H14 0.525857 -1.628596 -1.168273 H15 2.146762 -0.228883 -1.984752 H16 1.818078 1.010838 -3.106430 H17 -0.641774 2.550071 -1.138264 H18 0.503042 2.844767 -2.365315 H19 -0.880774 -2.880211 3.088084 H20 -1.139941 -1.431611 3.944290 <blank line>
We use higher energy level and basis set MP2/6-311++G(2d,2p) in order to get accurate energy result. Lower energy level has been used for optimization since the energy is sensitive to energy level while structure is not.
Multipoles calculation
Distributed Multipole Analysis (DMA) is a technique for describing a molecular charge distribution by using local multipoles at a number of sites within a molecule. It gives a much more accurate representation of the charge density than a single-point multipole expansion.
Generalized Distributed Multipole Analysis (GDMA) program was developed by Anthony Stone. It is a Fortran 90 program for performing Distributed Multipole Analysis of wavefunctions calculated using the Gaussian program system. That is, it calculates electric multipole moments at the atomic positions, or at other specified sites, that can give a very accurate representation of the electrostatic field of the molecule.
Multipole information can be extracted from formatted check file. Since check file is binary, need to run formchk to make it readable
(1)Do "formchk benzsp.chk". This will generate benzsp.fchk file.
(2) Make GDMA input file.
Title File benzsp.fchk density MP2 Angstrom AU Multipoles Limit 2 Radius H 0.31 Punch benzsp.punch Start Finish
GDMA program sets all the atom radii to be equal by default, except for hydrogen. The use of equal radii for all sites is the most efficient choice for convergence of the resulting multipole expansion of the electrostatic potential. Default radius is 0.65 Å. Different value may be explicitly specified. 0.325 Å for hydrogen, 1.11Å for chloride is found to give more acceptable values.
(3) Run GDMA to calculate multipoles of this ligand.
/opt/gdma-2.2/bin/gdma < gdmain > benzsp.gdmaout"
There are two output files benzsp.punch and benzsp.gdmaout.
Standard DMA
Positions and radii in angstrom
Multipole moments in atomic units, ea_0^k for rank k
C x = 0.640305 y = -0.000002 z = -0.000115
Maximum rank = 2 Relative radius = 0.650
Q00 = -0.101884
|Q1| = 0.024901 Q10 = 0.000007 Q11c = -0.024901 Q11s = -0.000018
|Q2| = 1.365955 Q20 = -1.283977 Q21c = 0.000260 Q21s = 0.375277
Q22c = 0.276408 Q22s = 0.000001
C x = -0.077336 y = 1.181820 z = 0.220245
Maximum rank = 2 Relative radius = 0.650
Q00 = -0.095143
|Q1| = 0.204753 Q10 = 0.005562 Q11c = -0.073651 Q11s = -0.190967
|Q2| = 1.225313 Q20 = -1.139120 Q21c = 0.041511 Q21s = 0.427129
Q22c = 0.084762 Q22s = -0.111577
C x = -1.442045 y = 1.184957 z = 0.229039
Maximum rank = 2 Relative radius = 0.650
Q00 = -0.091024
|Q1| = 0.176199 Q10 = -0.027643 Q11c = 0.050291 Q11s = -0.166592
|Q2| = 1.177708 Q20 = -1.106636 Q21c = -0.000588 Q21s = 0.379762
Q22c = 0.119889 Q22s = 0.061321
C x = -2.168671 y = 0.000011 z = -0.000002
Maximum rank = 2 Relative radius = 0.650
Q00 = 0.033606
|Q1| = 0.004956 Q10 = -0.000020 Q11c = 0.004956 Q11s = -0.000009
|Q2| = 1.025836 Q20 = -0.964500 Q21c = -0.000179 Q21s = 0.302654
Q22c = 0.174581 Q22s = 0.000026
....skipping.....
H x = -4.032047 y = -0.837065 z = -0.154879
Maximum rank = 2 Relative radius = 0.310
Q00 = 0.222435
|Q1| = 0.084255 Q10 = 0.009661 Q11c = 0.065456 Q11s = 0.052164
|Q2| = 0.181344 Q20 = -0.142929 Q21c = 0.017003 Q21s = 0.053053
Q22c = -0.029051 Q22s = 0.092245
H x = -4.032046 y = 0.836924 z = 0.155699
Maximum rank = 2 Relative radius = 0.310
Q00 = 0.222432
|Q1| = 0.084256 Q10 = -0.009709 Q11c = 0.065457 Q11s = -0.052156
|Q2| = 0.181345 Q20 = -0.142895 Q21c = -0.017130 Q21s = 0.053161
Q22c = -0.029030 Q22s = -0.092222
Total multipoles
referred to origin at x = 0.000000, y = 0.000000, z = 0.000000
Q00 = 0.999990
|Q1| = 1.655329 Q10 = 0.000477 Q11c = 1.655328 Q11s = -0.000178
|Q2| = 39.203832 Q20 = -29.420772 Q21c = -0.003923 Q21s = -2.843583
Q22c = 25.754080 Q22s = 0.000629
(4) Edit the multipoles from the GDMA output with poledit.x.
The Multipole Editing Facility can Provide :
(1) Multipole Parameters from GDMA Output
(2) Alter Local Coordinate Frame Definitions
(3) Removal of Intramolecular Polarization
Enter the Number of the Desired Choice : 1
Global Frame Cartesian Multipole Moments :
Site: 1 Name: C Atomic Number: 6
Coordinates: 0.640305 -0.000002 -0.000115
Charge: -0.10188
Dipole: -0.02490 -0.00002 0.00001
Quadrupole: 0.88136
0.00000 0.40261
0.00023 0.32500 -1.28398
Site: 2 Name: C Atomic Number: 6
Coordinates: -0.077336 1.181820 0.220245
Charge: -0.09514
Dipole: -0.07365 -0.19097 0.00556
Quadrupole: 0.64297
-0.09663 0.49615
0.03595 0.36990 -1.13912
Site: 3 Name: C Atomic Number: 6
Coordinates: -1.442045 1.184957 0.229039
Charge: -0.09102
Dipole: 0.05029 -0.16659 -0.02764
Quadrupole: 0.65714
0.05311 0.44949
-0.00051 0.32888 -1.10664
...skipping....
Local Frame Definition for Multipole Sites :
Site Name Axis Type Z Axis X Axis Y Axis
1 C Z-then-X 7 2 0
2 C Bisector 1 3 0
3 C Z-then-X 4 2 0
4 C Z-then-X 10 3 0
5 C Z-then-X 4 6 0
6 C Bisector 1 5 0
7 C Bisector 8 9 0
8 N Z-then-X 7 15 0
9 N Z-then-X 7 17 0
10 N Z-then-X 4 19 0
11 H Z-then-X 2 1 0
12 H Z-then-X 3 2 0
13 H Z-then-X 5 4 0
....skipping...
Enter Altered Local Frame Definition [<CR>=Exit] :
Atomic Polarizabilities for Multipole Sites :
Enter Atom Number & Polarizability Values [<CR>=Exit] :
Enter a Bond between Polarization Groups [<CR>=Exit] : (if the whole mole is one group - recommended for ligands - use default/Enter)
Average the Multipole Moments of Equivalent Atoms [N] : Y
Remove Multipole Components Zeroed by Symmetry [N] : Y
Site: 1 Name: C Atomic Number: 6
Local Frame: Z-then-X 7 2 0
Charge: -0.10188
Dipole: -0.00002 0.00000 -0.02490
Quadrupole: 0.46307
0.00000 -1.34443
0.00004 0.00000 0.88136
Site: 2 Name: C Atomic Number: 6
Local Frame: Bisector 1 3 0
Charge: -0.09514
Dipole: -0.02833 0.00000 0.19892
Quadrupole: 0.70208
0.00000 -1.21642
-0.01601 0.00000 0.51434
Site: 3 Name: C Atomic Number: 6
Local Frame: Z-then-X 4 2 0
Charge: -0.09102
Dipole: 0.13012 0.00000 0.11868
Quadrupole: 0.57375
0.00000 -1.17330
-0.08666 0.00000 0.59955
...skip...
This will generate benzsp.xyz and benzsp.key
benzsp.key has the electrostatic parameters
parameters ../amoeba.prm
(this comes from tinker.key in the current dir)
atom 1 1 C "ttt " 6 12.011 3
atom 2 2 C "ttt " 6 12.011 3
atom 3 3 C "ttt " 6 12.011 3
atom 4 4 C "ttt " 6 12.011 3
...
multipole 1 7 2 -0.10188
-0.00002 0.00000 -0.02490
0.46307
0.00000 -1.34443
0.00004 0.00000 0.88136
multipole 2 1 -3 -0.09514
-0.02833 0.00000 0.19892
0.70208
0.00000 -1.21642
-0.01601 0.00000 0.51434
...skipping...
polarize 1 1.334 0.390 2 6 7
polarize 2 1.334 0.390 1 3 11
polarize 3 1.334 0.390 2 4 12
polarize 4 1.334 0.390 3 5 10
polarize 5 1.334 0.390 4 6 13
...skipping...
Average the multipoles
Due to the symmetry of the ligand, we average the multipoles of these symmetric atoms.
- Change atom index
- Average multipoles
- Shift the index and move it to the parameter file
Refit the electrostatics with potential.x
This is useful to optimize the multipoles (after averaging over symmetric atoms,from one basis-set to another...)
Make sure your molecule is always oriented the same from QM to Tinker (always use standard orinetation, all "nosymm" in Gaussian potential calculation)
- Create grid points for molecule
- Compute electrostatic potential from QM formatted checkpoint file with cubegen
- Create potential file for grid points
- Fit Electrostatic parameters to target grid.
The TINKER Electrostatic Potential Facility Can :
(1) Get QM Potential from a Gaussian CUBE File
(2) Calculate the Model Potential for a System
(3) Compare the Model Potentials of Two Systems
(4) Compare a Model Potential to a Target Grid
(5) Fit Electrostatic Parameters to Target Grid
Enter the Number of the Desired Choice : 2
Output Potential Value at Each Grid Point [N] :Y
Average Electrostatic Potential over Atoms :
(Kcal/mole per unit charge)
Atom Points Potential
1 135 64.2195
2 371 59.3085
3 228 54.8976
4 302 52.9730
5 235 54.9886
6 366 59.4935
7 286 66.5887
8 523 65.5094
9 526 65.6609
10 654 49.3012
11 635 58.6693
12 3555 45.6758
13 3555 45.6982
14 624 58.6372
15 1243 62.0622
16 1637 64.5757
17 1230 62.0704
18 1645 64.6416
19 1071 48.1094
20 1074 48.0477
Electrostatic Potential over all Grid Points :
Average Magnitude for Potential : 54.3511
benzsp.pot and benzsp.grid will be generated.
benzsp.grid has the coordinates of grid
-1.34113200 -0.00020800 -3.20007300 -1.38600600 0.19213500 -3.19397200 -1.61966900 0.01881500 -3.18787100 -1.53376000 -0.28251900 -3.18177000 -1.22361200 -0.37674500 -3.17566900 -0.94649500 -0.19658800 -3.16956800 -0.87661000 0.13078800 -3.16346700 -1.04108100 0.42578800 -3.15736600 -1.35499000 0.55638800 -3.15126500 -1.68754100 0.47771100 -3.14516400 -1.92050000 0.22579500 -3.13906300 -1.25966200 -0.73008500 -3.11465800 -0.92533300 -0.63616200 -3.10855700 -0.66777100 -0.40245600 -3.10245600 ...skipping...
benzsp.pot has the potential at each grid points (from tinker)
19895
1 -1.341132 -0.000208 -3.200073 70.7873
2 -1.386006 0.192135 -3.193972 70.3143
3 -1.619669 0.018815 -3.187871 72.7352
4 -1.533760 -0.282519 -3.181770 73.6782
5 -1.223612 -0.376745 -3.175669 71.7168
6 -0.946495 -0.196588 -3.169568 69.0251
7 -0.876610 0.130788 -3.163467 67.5038
8 -1.041081 0.425788 -3.157366 67.5183
9 -1.354990 0.556388 -3.151265 68.9467
10 -1.687541 0.477711 -3.145164 71.3468
11 -1.920500 0.225795 -3.139063 74.0949
12 -1.259662 -0.730085 -3.114658 74.0606
...skipping...
/opt/g03/bin/cubegen 0 potential=MP2 benzsp.fchk benzsp.cube -5 h < benzsp.grid
This will compute the potential of the tinker grid from QM
-1.341132000000 -0.000208000000 -3.200073000000 0.112800371358 -1.386006000000 0.192135000000 -3.193972000000 0.112181402714 -1.619669000000 0.018815000000 -3.187871000000 0.115556191658 -1.533760000000 -0.282519000000 -3.181770000000 0.116842473623 -1.223612000000 -0.376745000000 -3.175669000000 0.114038580816 -0.946495000000 -0.196588000000 -3.169568000000 0.110351219561 -0.876610000000 0.130788000000 -3.163467000000 0.108378055681 -1.041081000000 0.425788000000 -3.157366000000 0.108460613005 -1.354990000000 0.556388000000 -3.151265000000 0.110406541871 -1.687541000000 0.477711000000 -3.145164000000 0.113700818337 -1.920500000000 0.225795000000 -3.139063000000 0.117550862437 -1.259662000000 -0.730085000000 -3.114658000000 0.117304867056 -0.925333000000 -0.636162000000 -3.108557000000 0.112718952139 -0.667771000000 -0.402456000000 -3.102456000000 0.109223962529 -0.536946000000 -0.079718000000 -3.096355000000 0.107108578011 ...skipping...
potential.x to take QM potential from cube file (1) and then fit the parameters to the grid (5)
New potential file converted from cube output which is consistent with tinker pot file in format
19895 sp energy potential=MP2
1 -1.341132 -0.000208 -3.200073 70.7833
2 -1.386006 0.192135 -3.193972 70.3949
3 -1.619669 0.018815 -3.187871 72.5126
4 -1.533760 -0.282519 -3.181770 73.3198
5 -1.223612 -0.376745 -3.175669 71.5603
6 -0.946495 -0.196588 -3.169568 69.2464
7 -0.876610 0.130788 -3.163467 68.0083
8 -1.041081 0.425788 -3.157366 68.0601
9 -1.354990 0.556388 -3.151265 69.2812
10 -1.687541 0.477711 -3.145164 71.3483
11 -1.920500 0.225795 -3.139063 73.7643
12 -1.259662 -0.730085 -3.114658 73.6099
13 -0.925333 -0.636162 -3.108557 70.7322
14 -0.667771 -0.402456 -3.102456 68.5391
15 -0.536946 -0.079718 -3.096355 67.2116
16 -1.668816 0.856317 -3.065850 70.4540
...skipping...
Enter RMS Gradient Termination Criterion [0.001] : 0.1
Average Electrostatic Potential over Atoms :
(Kcal/mole per unit charge)
Atom Points Potential Target RMS Diff
1 135 64.2195 64.4504 0.3508
2 371 59.3085 60.0373 0.8938
3 228 54.8976 56.0802 1.2937
4 302 52.9730 53.8936 0.9659
5 235 54.9886 56.0704 1.1716
6 366 59.4935 60.1774 0.8223
7 286 66.5887 66.4829 0.2056
8 523 65.5094 65.3357 0.3199
...skipping....
Electrostatic Potential over all Grid Points :
Average Magnitude for Potential : 54.3511
Average Magnitude for Target : 54.4149
Average Signed Potential Difference : -0.0639
Average Unsigned Potential Difference : 0.5162
Root Mean Square Potential Difference : 0.6756
Potential Fitting of Electrostatic Parameters :
Parameter Atom Type Category Value Fixed
-- 1 Monopole -0.05287 X
1 1 X-Dipole -0.00001
-- 1 Y-Dipole 0.00000 X
2 1 Z-Dipole -0.02333
3 1 XX-Quad 0.16559
-- 1 XY-Quad 0.00000 X
4 1 XZ-Quad -0.00011
5 1 YY-Quad -0.51058
-- 1 YZ-Quad 0.00000 X
-- 1 ZZ-Quad 0.34499
-- 2 Monopole -0.38438 X
...skipping...
Optimally Conditioned Variable Metric Optimization :
VM Iter F Value G RMS F Move X Move Angle FG Call
0 2250.6724 20301.4582 1
1 1857.3986 18441.9488 393.2738 0.0002 0.0000 2
2 0.8428 63.0015 1856.5558 0.0020 0.0000 3
3 0.8388 62.2482 0.0039 0.0000 0.4472 4
4 0.6737 61.3801 0.1652 0.0001 0.0001 5
5 0.6699 57.8278 0.0038 0.0000 12.0351 6
...skipping...
16 1637 63.3915 63.7087 0.3363
17 1230 61.7354 61.8744 0.1606
18 1645 63.4573 63.7545 0.3150
19 1071 48.1338 47.8362 0.3167
20 1074 48.0967 47.7956 0.3196
Electrostatic Potential over all Grid Points :
Average Magnitude for Potential : 54.4084
Average Magnitude for Target : 54.4149
Average Signed Potential Difference : -0.0065
Average Unsigned Potential Difference : 0.1797
Root Mean Square Potential Difference : 0.2223
References
- ↑ Arieh Warshel, Mitsunori Kato, and Andrei V. Pisliakov. JCTC. 2007