A series of Python3 script to lower the barrier of computing and simulating molecular and material systems.
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AMBER SQM VERSION 19
By
Ross C. Walker, Michael F. Crowley, Scott Brozell,
Tim Giese, Andreas W. Goetz,
Tai-Sung Lee and David A. Case
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QM CALCULATION INFO
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| QMMM: Citation for AMBER QMMM Run:
| QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
QMMM: SINGLET STATE CALCULATION
QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 12
| QMMM: *** Selected Hamiltonian ***
| QMMM: AM1
| QMMM: *** Parameter sets in use ***
| QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: *** SCF convergence criteria ***
| QMMM: Energy change : 0.1D-09 kcal/mol
| QMMM: Error matrix |FP-PF| : 0.1D+00 au
| QMMM: Density matrix change : 0.5D-06
| QMMM: Maximum number of SCF cycles : 1000
| QMMM: *** Diagonalization Routine Information ***
| QMMM: Pseudo diagonalizations are allowed.
| QMMM: Auto diagonalization routine selection is in use.
| QMMM:
| QMMM: Timing diagonalization routines:
| QMMM: norbs = 20
| QMMM: diag iterations used for timing = 20
| QMMM:
| QMMM: Internal diag routine = 0.002230 seconds
| QMMM: Dspev diag routine = 0.008533 seconds
| QMMM: Dspevd diag routine = 0.003488 seconds
| QMMM: Dspevx diag routine = 0.009568 seconds
| QMMM: Dsyev diag routine = 0.003297 seconds
| QMMM: Dsyevd diag routine = 0.002872 seconds
| QMMM: Dsyevr diag routine = 0.003359 seconds
| QMMM:
| QMMM: Pseudo diag routine = 0.000374 seconds
| QMMM:
| QMMM: Using internal diagonalization routine (diag_routine=1).
QMMM: QM Region Cartesian Coordinates (*=link atom)
QMMM: QM_NO. MM_NO. ATOM X Y Z
QMMM: 1 1 C -3.9390 0.7940 0.0000
QMMM: 2 2 O -3.8510 2.0130 0.0000
QMMM: 3 3 N -5.1590 0.2090 0.0000
QMMM: 4 4 N -2.8150 0.0390 0.0000
QMMM: 5 5 H -6.0150 0.7840 0.0000
QMMM: 6 6 H -5.2530 -0.8180 0.0000
QMMM: 7 7 H -1.8860 0.4850 0.0000
QMMM: 8 8 H -2.8700 -0.9900 0.0000
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RESULTS
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iter sqm energy rms gradient
---- ------------------- -----------------------
xmin 10 -44.2844 kcal/mol 1.4147 kcal/(mol*A)
xmin 20 -44.9536 kcal/mol 0.3316 kcal/(mol*A)
xmin 30 -44.9570 kcal/mol 0.0088 kcal/(mol*A)
... geometry converged !
Final MO eigenvalues (eV):
-39.2550 -34.3126 -33.2840 -22.3312 -18.7079 -18.5034 -16.0576 -15.2042
-15.2036 -11.3580 -10.9180 -10.6248 1.5705 1.9352 3.4710 5.1127
5.2857 5.3752 6.3604 7.2003
Heat of formation = -44.95702535 kcal/mol ( -1.94948291 eV)
Total SCF energy = -21172.22001634 kcal/mol ( -918.09635386 eV)
Electronic energy = -58014.07035379 kcal/mol ( -2515.67886708 eV)
Core-core repulsion = 36841.85033745 kcal/mol ( 1597.58251322 eV)
Atomic Charges for Step 1 :
Atom Element Mulliken Charge
1 C 0.353
2 O -0.400
3 N -0.402
4 N -0.402
5 H 0.222
6 H 0.203
7 H 0.222
8 H 0.203
Total Mulliken Charge = -0.000
X Y Z TOTAL
QM DIPOLE -0.280 -3.595 0.017 3.606
Final Structure
QMMM: QM Region Cartesian Coordinates (*=link atom)
QMMM: QM_NO. MM_NO. ATOM X Y Z
QMMM: 1 1 C -3.9378 0.7722 -0.0022
QMMM: 2 2 O -3.8403 2.0240 -0.0082
QMMM: 3 3 N -5.1945 0.1668 -0.1509
QMMM: 4 4 N -2.7900 -0.0191 0.1532
QMMM: 5 5 H -5.9606 0.7897 -0.0329
QMMM: 6 6 H -5.3258 -0.7477 0.2077
QMMM: 7 7 H -1.9367 0.4764 0.0298
QMMM: 8 8 H -2.8022 -0.9463 -0.1966
--------- Calculation Completed ----------