Hello,
I am attempting to run partial charge calculations for a set of molecules.
I've found that sqm fails frequently on nitriles connected to aromatic
systems. Please find the relevant files below my signature.
My run command is:
antechamber -i molecule.sdf -fi sdf -o charged.mol2 -fo mol2 -pf yes -c bcc
-nc 0
I'm running antechamber and sqm from
https://github.com/choderalab/ambermini/, which uses AmberTools16
I've also seen convergence failures on the following molecules from the
ZINC database, most of which contain aromatic-adjacent nitriles:
ZINC00335972 <
http://zinc15.docking.org/substances/ZINC000000335972/>
ZINC35326424 <
http://zinc15.docking.org/substances/ZINC000035326424/>
ZINC00160396 (example in this email)
<
http://zinc15.docking.org/substances/ZINC000000160396/>
ZINC13130634
ZINC28114756
ZINC10022957
ZINC14143999
ZINC24528707
ZINC01615096 (not aromatic)
Does anyone have suggestions about how to handle this?
Thanks,
Jeff Wagner
molecule.sdf:
ZINC00160396
RDKit 3D
33 35 0 0 0 0 0 0 0 0999 V2000
-3.7214 5.0899 -3.7838 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.1071 4.9687 -2.0856 S 0 0 0 0 0 0 0 0 0 0 0 0
-2.1317 3.5072 -2.2165 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.4877 3.0611 -1.1471 N 0 0 0 0 0 0 0 0 0 0 0 0
-0.7468 1.9670 -1.2108 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.6441 1.2887 -2.4145 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.3356 1.7793 -3.5135 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.0596 2.8797 -3.3818 N 0 0 0 0 0 0 0 0 0 0 0 0
-1.2462 0.9640 -5.0436 Cl 0 0 0 0 0 0 0 0 0 0 0 0
-0.0179 1.4678 0.0101 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.5281 1.8193 0.9069 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0021 -0.0041 0.0020 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0175 -1.1399 -0.0042 N 0 0 0 0 0 0 0 0 0 0 0 0
1.3959 1.9894 -0.0006 C 0 0 0 0 0 0 0 0 0 0 0 0
2.3476 1.3071 -0.6963 C 0 0 0 0 0 0 0 0 0 0 0 0
3.6643 1.8016 -0.7011 C 0 0 0 0 0 0 0 0 0 0 0 0
4.7019 1.1596 -1.3924 C 0 0 0 0 0 0 0 0 0 0 0 0
5.9569 1.6881 -1.3593 C 0 0 0 0 0 0 0 0 0 0 0 0
6.2256 2.8571 -0.6495 C 0 0 0 0 0 0 0 0 0 0 0 0
5.2428 3.5069 0.0331 C 0 0 0 0 0 0 0 0 0 0 0 0
3.9369 2.9920 0.0225 C 0 0 0 0 0 0 0 0 0 0 0 0
2.8830 3.6183 0.7068 C 0 0 0 0 0 0 0 0 0 0 0 0
1.6768 3.1023 0.6629 N 0 0 0 0 0 0 0 0 0 0 0 0
-2.8788 5.1796 -4.4694 H 0 0 0 0 0 0 0 0 0 0 0 0
-4.2944 4.1953 -4.0276 H 0 0 0 0 0 0 0 0 0 0 0 0
-4.3608 5.9676 -3.8771 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.0424 0.3955 -2.4949 H 0 0 0 0 0 0 0 0 0 0 0 0
2.0963 0.4043 -1.2332 H 0 0 0 0 0 0 0 0 0 0 0 0
4.5075 0.2531 -1.9463 H 0 0 0 0 0 0 0 0 0 0 0 0
6.7561 1.1938 -1.8917 H 0 0 0 0 0 0 0 0 0 0 0 0
7.2300 3.2539 -0.6404 H 0 0 0 0 0 0 0 0 0 0 0 0
5.4662 4.4120 0.5783 H 0 0 0 0 0 0 0 0 0 0 0 0
3.0634 4.5253 1.2645 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
1 24 1 0
1 25 1 0
1 26 1 0
2 3 1 0
3 8 2 0
3 4 1 0
4 5 2 0
5 6 1 0
5 10 1 0
6 7 2 0
6 27 1 0
7 8 1 0
7 9 1 0
10 11 1 0
10 12 1 0
10 14 1 0
12 13 3 0
14 23 1 0
14 15 2 0
15 16 1 0
15 28 1 0
16 21 2 0
16 17 1 0
17 18 2 0
17 29 1 0
18 19 1 0
18 30 1 0
19 20 2 0
19 31 1 0
20 21 1 0
20 32 1 0
21 22 1 0
22 23 2 0
22 33 1 0
M END
$$$$
sqm.in:
Run semi-empirical minimization
&qmmm
qm_theory='AM1', grms_tol=0.0005,
scfconv=1.d-10, qmcharge=0,
/
6 C1 -3.7210 5.0900 -3.7840
16 S1 -3.1070 4.9690 -2.0860
6 C2 -2.1320 3.5070 -2.2160
7 N1 -1.4880 3.0610 -1.1470
6 C3 -0.7470 1.9670 -1.2110
6 C4 -0.6440 1.2890 -2.4140
6 C5 -1.3360 1.7790 -3.5140
7 N2 -2.0600 2.8800 -3.3820
17 Cl1 -1.2460 0.9640 -5.0440
6 C6 -0.0180 1.4680 0.0100
1 H1 -0.5280 1.8190 0.9070
6 C7 0.0020 -0.0040 0.0020
7 N3 0.0180 -1.1400 -0.0040
6 C8 1.3960 1.9890 -0.0010
6 C9 2.3480 1.3070 -0.6960
6 C10 3.6640 1.8020 -0.7010
6 C11 4.7020 1.1600 -1.3920
6 C12 5.9570 1.6880 -1.3590
6 C13 6.2260 2.8570 -0.6490
6 C14 5.2430 3.5070 0.0330
6 C15 3.9370 2.9920 0.0220
6 C16 2.8830 3.6180 0.7070
7 N4 1.6770 3.1020 0.6630
1 H2 -2.8790 5.1800 -4.4690
1 H3 -4.2940 4.1950 -4.0280
1 H4 -4.3610 5.9680 -3.8770
1 H5 -0.0420 0.3960 -2.4950
1 H6 2.0960 0.4040 -1.2330
1 H7 4.5080 0.2530 -1.9460
1 H8 6.7560 1.1940 -1.8920
1 H9 7.2300 3.2540 -0.6400
1 H10 5.4660 4.4120 0.5780
1 H11 3.0630 4.5250 1.2640
sqm.out:
--------------------------------------------------------
AMBER SQM VERSION 14
By
Ross C. Walker, Michael F. Crowley, Scott Brozell,
Tim Giese, Andreas W. Goetz,
Tai-Sung Lee and David A. Case
--------------------------------------------------------
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
| 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 = 54
| QMMM: *** Selected Hamiltonian ***
| QMMM: AM1
| QMMM: *** Parameter sets in use ***
| QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: S : M.J.S.DEWAR et al. INORG. CHEM., 29, 3881, (1990)
| QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: Cl: M.J.S.DEWAR et al. THEOCHEM, 180, 1, (1988)
| 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 = 99
| QMMM: diag iterations used for timing = 15
| QMMM:
| QMMM: Internal diag routine = 0.028516 seconds
| QMMM: Dspev diag routine = 0.031480 seconds
| QMMM: Dspevd diag routine = 0.023209 seconds
| QMMM: Dspevx diag routine = 0.108077 seconds
| QMMM: Dsyev diag routine = 0.038986 seconds
| QMMM: Dsyevd diag routine = 0.028374 seconds
| QMMM: Dsyevr diag routine = 0.030189 seconds
| QMMM:
| QMMM: Pseudo diag routine = 0.013546 seconds
| QMMM:
| QMMM: Using dspevd routine (diag_routine=3).
QMMM: QM Region Cartesian Coordinates (*=link atom)
QMMM: QM_NO. MM_NO. ATOM X Y Z
QMMM: 1 1 C -3.7210 5.0900 -3.7840
QMMM: 2 2 S -3.1070 4.9690 -2.0860
QMMM: 3 3 C -2.1320 3.5070 -2.2160
QMMM: 4 4 N -1.4880 3.0610 -1.1470
QMMM: 5 5 C -0.7470 1.9670 -1.2110
QMMM: 6 6 C -0.6440 1.2890 -2.4140
QMMM: 7 7 C -1.3360 1.7790 -3.5140
QMMM: 8 8 N -2.0600 2.8800 -3.3820
QMMM: 9 9 Cl -1.2460 0.9640 -5.0440
QMMM: 10 10 C -0.0180 1.4680 0.0100
QMMM: 11 11 H -0.5280 1.8190 0.9070
QMMM: 12 12 C 0.0020 -0.0040 0.0020
QMMM: 13 13 N 0.0180 -1.1400 -0.0040
QMMM: 14 14 C 1.3960 1.9890 -0.0010
QMMM: 15 15 C 2.3480 1.3070 -0.6960
QMMM: 16 16 C 3.6640 1.8020 -0.7010
QMMM: 17 17 C 4.7020 1.1600 -1.3920
QMMM: 18 18 C 5.9570 1.6880 -1.3590
QMMM: 19 19 C 6.2260 2.8570 -0.6490
QMMM: 20 20 C 5.2430 3.5070 0.0330
QMMM: 21 21 C 3.9370 2.9920 0.0220
QMMM: 22 22 C 2.8830 3.6180 0.7070
QMMM: 23 23 N 1.6770 3.1020 0.6630
QMMM: 24 24 H -2.8790 5.1800 -4.4690
QMMM: 25 25 H -4.2940 4.1950 -4.0280
QMMM: 26 26 H -4.3610 5.9680 -3.8770
QMMM: 27 27 H -0.0420 0.3960 -2.4950
QMMM: 28 28 H 2.0960 0.4040 -1.2330
QMMM: 29 29 H 4.5080 0.2530 -1.9460
QMMM: 30 30 H 6.7560 1.1940 -1.8920
QMMM: 31 31 H 7.2300 3.2540 -0.6400
QMMM: 32 32 H 5.4660 4.4120 0.5780
QMMM: 33 33 H 3.0630 4.5250 1.2640
--------------------------------------------------------------------------------
RESULTS
--------------------------------------------------------------------------------
iter sqm energy rms gradient
---- ------------------- -----------------------
xmin 10 125.4581 kcal/mol 0.7404 kcal/(mol*A)
xmin 20 125.3456 kcal/mol 0.0559 kcal/(mol*A)
xmin 30 125.3426 kcal/mol 0.1287 kcal/(mol*A)
xmin 40 125.3361 kcal/mol 0.0743 kcal/(mol*A)
xmin 50 125.3295 kcal/mol 0.0570 kcal/(mol*A)
xmin 60 125.3271 kcal/mol 0.0585 kcal/(mol*A)
xmin 70 125.3260 kcal/mol 0.0648 kcal/(mol*A)
xmin 80 125.3247 kcal/mol 0.0813 kcal/(mol*A)
xmin 90 125.3146 kcal/mol 0.1057 kcal/(mol*A)
xmin 100 125.3130 kcal/mol 0.0339 kcal/(mol*A)
xmin 110 125.2865 kcal/mol 0.0630 kcal/(mol*A)
xmin 120 125.2664 kcal/mol 0.0958 kcal/(mol*A)
QMMM: ERROR!
QMMM: Unable to achieve self consistency to the tolerances specified
QMMM: No convergence in SCF after 1000 steps.
QMMM: E = -0.5383E+06 DeltaE = 0.2202E+00 DeltaP = 0.3514E-01
QMMM: Smallest DeltaE = 0.8312E-01 DeltaP = 0.4489E-01 Step = 8
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Received on Fri Nov 02 2018 - 11:00:02 PDT
