Re: [AMBER] Non-convergence when calculating partial charges for aromatic-adjacent nitriles

From: James Kress <jimkress_58.kressworks.org>
Date: Fri, 2 Nov 2018 15:02:27 -0400

Did you notice that you ran out of SCF steps?

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

It appears your system wavefunction is divergent. Have you looked to see
why that might be the case?

Jim Kress


-----Original Message-----
From: Jeffrey Wagner <jwagnerjpl.gmail.com>
Sent: Friday, November 02, 2018 1:51 PM
To: amber.ambermd.org
Subject: [AMBER] Non-convergence when calculating partial charges for
aromatic-adjacent nitriles

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 - 12:30:02 PDT
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