sqm failure

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/Jochuan/Desktop/Ligands1.pdb

> ui tool show "Dock Prep"

Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to Ligands1.pdb #1  
---  
notes | Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
1 hydrogen bonds  
48 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue FMN (net charge -1) with am1-bcc method  
Running ANTECHAMBER command: C:/Program
Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\Jochuan\AppData\Local\Temp\tmpvfnotp2u\ante.in.mol2 -fi mol2 -o
C:\Users\Jochuan\AppData\Local\Temp\tmpvfnotp2u\ante.out.mol2 -fo mol2 -c bcc
-nc -1 -j 5 -s 2 -dr n  
(FMN) ``  
(FMN) `Welcome to antechamber 20.0: molecular input file processor.`  
(FMN) ``  
(FMN) `Info: Finished reading file
(C:\Users\Jochuan\AppData\Local\Temp\tmpvfnotp2u\ante.in.mol2); atoms read
(47), bonds read (49).`  
(FMN) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(FMN) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(FMN) `bash.exe: warning: could not find /tmp, please create!`  
(FMN) ``  
(FMN) ``  
(FMN) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(FMN) `bash.exe: warning: could not find /tmp, please create!`  
(FMN) `Info: Total number of electrons: 234; net charge: -1`  
(FMN) ``  
(FMN) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`  
(FMN) `bash.exe: warning: could not find /tmp, please create!`  
(FMN) ``  
(FMN) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/am1bcc" -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program
Files/ChimeraX/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1`  
(FMN) `bash.exe: warning: could not find /tmp, please create!`  
(FMN) ``  
(FMN) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -f ac -p
bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(FMN) `bash.exe: warning: could not find /tmp, please create!`  
(FMN) ``  
Charges for residue FMN determined  
Assigning partial charges to residue HEM[FE] (net charge +2) with am1-bcc
method  
Assigning partial charges to residue HEM[non-FE] (net charge -4) with am1-bcc
method  
Running ANTECHAMBER command: C:/Program
Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\Jochuan\AppData\Local\Temp\tmpxdpcos_t\ante.in.mol2 -fi mol2 -o
C:\Users\Jochuan\AppData\Local\Temp\tmpxdpcos_t\ante.out.mol2 -fo mol2 -c bcc
-nc -4 -j 5 -s 2 -dr n  
(HEM[non-FE]) ``  
(HEM[non-FE]) `Welcome to antechamber 20.0: molecular input file processor.`  
(HEM[non-FE]) ``  
(HEM[non-FE]) `Info: Finished reading file
(C:\Users\Jochuan\AppData\Local\Temp\tmpxdpcos_t\ante.in.mol2); atoms read
(74), bonds read (78).`  
(HEM[non-FE]) `Info: Determining atomic numbers from atomic symbols which are
case sensitive.`  
(HEM[non-FE]) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype"
-j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(HEM[non-FE]) `bash.exe: warning: could not find /tmp, please create!`  
(HEM[non-FE]) ``  
(HEM[non-FE]) ``  
(HEM[non-FE]) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype"
-i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(HEM[non-FE]) `bash.exe: warning: could not find /tmp, please create!`  
(HEM[non-FE]) `Info: Total number of electrons: 300; net charge: -4`  
(HEM[non-FE]) ``  
(HEM[non-FE]) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i
sqm.in -o sqm.out`  
(HEM[non-FE]) `bash.exe: warning: could not find /tmp, please create!`  
  
Contents of sqm.out:

    
    
                --------------------------------------------------------
                                 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
     
                --------------------------------------------------------
     
    
    --------------------------------------------------------------------------------
      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 =108
    
    | QMMM: *** Selected Hamiltonian *** 
    | QMMM: AM1         
    
    | QMMM: *** Parameter sets in use ***
    | QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    | QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    | QMMM: O : 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-07 kcal/mol
    | QMMM: Error matrix |FP-PF|         :  0.1D+00 au
    | QMMM: Density matrix change        :  0.5D-05
    | 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 =      200
    | QMMM:    diag iterations used for timing =        5
    | QMMM:
    | QMMM:              Internal diag routine = 0.042880 seconds
    | QMMM:                 Dspev diag routine = 0.033768 seconds
    | QMMM:                Dspevd diag routine = 0.028304 seconds
    | QMMM:                Dspevx diag routine = 0.127756 seconds
    | QMMM:                 Dsyev diag routine = 0.037924 seconds
    | QMMM:                Dsyevd diag routine = 0.032272 seconds
    | QMMM:                Dsyevr diag routine = 0.033834 seconds
    | QMMM:
    | QMMM:                Pseudo diag routine = 0.020911 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        2.0170   -0.9560    0.2030
      QMMM:     2        2      C       -0.2840    5.7350    6.9290
      QMMM:     3        3      C       -6.2590    5.5740    1.9290
      QMMM:     4        4      C       -2.6470   -0.2810   -2.2060
      QMMM:     5        5      N        0.0600    1.6530    2.1300
      QMMM:     6        6      C        2.6420   -0.2510   -0.9900
      QMMM:     7        7      C       -0.2150    7.1550    6.9690
      QMMM:     8        8      C       -6.3540    6.9400    1.4510
      QMMM:     9        9      C       -1.8430    0.3000   -3.3810
      QMMM:    10       10      N       -0.5960    3.6280    3.9490
      QMMM:    11       11      C        3.1430   -1.2150   -2.0430
      QMMM:    12       12      C       -1.7860   -0.6340   -4.5780
      QMMM:    13       13      N       -2.4390    2.0440    0.8320
      QMMM:    14       14      C       -0.7500    0.3500    0.1930
      QMMM:    15       15      C        1.6070    2.5250    3.8480
      QMMM:    16       16      C       -2.4470    4.9440    4.8930
      QMMM:    17       17      C       -4.4150    3.4700    0.7160
      QMMM:    18       18      C        3.6410    0.4460    2.5870
      QMMM:    19       19      C        2.3940    4.6180    6.1180
      QMMM:    20       20      C       -5.2120    6.3850    4.7410
      QMMM:    21       21      C       -4.9570    1.9340   -1.9880
      QMMM:    22       22      C        0.2250    0.6910    1.1360
      QMMM:    23       23      C        0.7350    3.4750    4.3590
      QMMM:    24       24      C       -3.4020    4.5940    3.9580
      QMMM:    25       25      C       -3.5780    2.4790    0.2090
      QMMM:    26       26      O        3.7700   -2.2290   -1.6790
      QMMM:    27       27      O       -2.8270   -1.2380   -4.9120
      QMMM:    28       28      C        1.5300    0.1030    1.1740
      QMMM:    29       29      C        1.0550    4.3740    5.4460
      QMMM:    30       30      C       -4.5990    5.4030    3.7590
      QMMM:    31       31      C       -3.8520    1.6950   -0.9790
      QMMM:    32       32      O        2.9120   -0.9520   -3.2350
      QMMM:    33       33      O       -0.7000   -0.7620   -5.1860
      QMMM:    34       34      C        2.1950    0.6990    2.1940
      QMMM:    35       35      C       -0.0920    4.9980    5.7740
      QMMM:    36       36      C       -5.1050    5.0890    2.5300
      QMMM:    37       37      C       -2.8840    0.7520   -1.0780
      QMMM:    38       38      C        1.2810    1.6600    2.8000
      QMMM:    39       39      C       -1.1180    4.5520    4.8440
      QMMM:    40       40      C       -4.2280    4.0630    1.9740
      QMMM:    41       41      C       -1.9960    0.9990    0.0470
      QMMM:    42       42      N       -3.1610    3.7850    2.8460
      QMMM:    43       43      H        1.1780   -1.5680   -0.1280
      QMMM:    44       44      H        2.7620   -1.5860    0.6890
      QMMM:    45       45      H       -0.4970    5.2060    7.8460
      QMMM:    46       46      H       -7.1080    4.9170    1.8150
      QMMM:    47       47      H       -2.0990   -1.1280   -1.7940
      QMMM:    48       48      H       -3.6120   -0.6290   -2.5750
      QMMM:    49       49      H        1.8930    0.4000   -1.4420
      QMMM:    50       50      H        3.4770    0.3580   -0.6430
      QMMM:    51       51      H       -2.3080    1.2350   -3.6920
      QMMM:    52       52      H       -0.8270    0.5060   -3.0450
      QMMM:    53       53      H       -0.5340   -0.4720   -0.4740
      QMMM:    54       54      H        2.5920    2.4500    4.2840
      QMMM:    55       55      H       -2.7570    5.5660    5.7200
      QMMM:    56       56      H       -5.2480    3.7980    0.1120
      QMMM:    57       57      H       -0.4010    7.5000    7.9860
      QMMM:    58       58      H       -0.9670    7.5740    6.3010
      QMMM:    59       59      H        0.7750    7.4800    6.6500
      QMMM:    60       60      H       -7.3400    7.1060    1.0180
      QMMM:    61       61      H       -5.5900    7.1130    0.6930
      QMMM:    62       62      H       -6.2020    7.6280    2.2830
      QMMM:    63       63      H        3.9030    1.0760    3.4370
      QMMM:    64       64      H        4.2930    0.6820    1.7460
      QMMM:    65       65      H        3.7650   -0.6020    2.8600
      QMMM:    66       66      H        3.1730    4.0720    5.5860
      QMMM:    67       67      H        2.6200    5.6840    6.1000
      QMMM:    68       68      H        2.3500    4.2730    7.1510
      QMMM:    69       69      H       -4.8350    6.1810    5.7430
      QMMM:    70       70      H       -6.2970    6.2780    4.7320
      QMMM:    71       71      H       -4.9450    7.4020    4.4530
      QMMM:    72       72      H       -5.5920    2.7510   -1.6450
      QMMM:    73       73      H       -4.5190    2.1940   -2.9520
      QMMM:    74       74      H       -5.5550    1.0290   -2.0930
    
    --------------------------------------------------------------------------------
      RESULTS
    --------------------------------------------------------------------------------
    
          iter         sqm energy              rms gradient
          ----    -------------------    -----------------------
    xmin    10      268.3907 kcal/mol        5.4804 kcal/(mol*A)
    xmin    20      259.3807 kcal/mol        1.6041 kcal/(mol*A)
    xmin    30      256.4042 kcal/mol        2.0757 kcal/(mol*A)
    xmin    40      252.3508 kcal/mol        1.9851 kcal/(mol*A)
    xmin    50      245.2949 kcal/mol        3.8747 kcal/(mol*A)
    xmin    60      235.1987 kcal/mol        5.8881 kcal/(mol*A)
    xmin    70      227.9221 kcal/mol        4.1785 kcal/(mol*A)
    xmin    80      223.2037 kcal/mol        3.4906 kcal/(mol*A)
    xmin    90      216.0103 kcal/mol        2.7717 kcal/(mol*A)
    xmin   100      209.9789 kcal/mol        2.5419 kcal/(mol*A)
    xmin   110      206.9888 kcal/mol        1.1996 kcal/(mol*A)
    xmin   120      214.2557 kcal/mol       15.6989 kcal/(mol*A)
    xmin   130      204.5176 kcal/mol        0.8943 kcal/(mol*A)
    xmin   140      204.1155 kcal/mol        0.6957 kcal/(mol*A)
    xmin   150      203.7882 kcal/mol        0.6402 kcal/(mol*A)
    xmin   160      203.5144 kcal/mol        0.5982 kcal/(mol*A)
    xmin   170      203.2735 kcal/mol        0.5410 kcal/(mol*A)
    xmin   180      203.0427 kcal/mol        0.4802 kcal/(mol*A)
    xmin   190      202.7898 kcal/mol        0.4218 kcal/(mol*A)
    xmin   200      202.3646 kcal/mol        1.2430 kcal/(mol*A)
    xmin   210      201.7301 kcal/mol        1.3950 kcal/(mol*A)
    xmin   220      201.0947 kcal/mol        1.2252 kcal/(mol*A)
    xmin   230      200.6552 kcal/mol        0.9477 kcal/(mol*A)
    xmin   240      204.7498 kcal/mol        1.3971 kcal/(mol*A)
    xmin   250      204.2208 kcal/mol        1.0036 kcal/(mol*A)
    xmin   260      203.7487 kcal/mol        2.6816 kcal/(mol*A)
    xmin   270      198.7344 kcal/mol        1.3866 kcal/(mol*A)
    xmin   280      198.0387 kcal/mol        0.3614 kcal/(mol*A)
    xmin   290      197.6518 kcal/mol        0.5336 kcal/(mol*A)
    xmin   300      197.2021 kcal/mol        0.9214 kcal/(mol*A)
    xmin   310      196.9694 kcal/mol        0.5620 kcal/(mol*A)
    xmin   320      196.6372 kcal/mol        0.9932 kcal/(mol*A)
    xmin   330      197.1885 kcal/mol        3.6727 kcal/(mol*A)
    xmin   340      195.7937 kcal/mol        0.6748 kcal/(mol*A)
    xmin   350      195.5212 kcal/mol        0.1586 kcal/(mol*A)
    xmin   360      195.1063 kcal/mol        0.2822 kcal/(mol*A)
    xmin   370      194.9517 kcal/mol        0.5316 kcal/(mol*A)
    xmin   380      194.8405 kcal/mol        0.3024 kcal/(mol*A)
    xmin   390      194.6821 kcal/mol        0.2455 kcal/(mol*A)
    xmin   400      194.6005 kcal/mol        0.4069 kcal/(mol*A)
    xmin   410      194.4019 kcal/mol        0.4889 kcal/(mol*A)
    xmin   420      194.3328 kcal/mol        0.2742 kcal/(mol*A)
    xmin   430      194.1717 kcal/mol        0.4448 kcal/(mol*A)
    xmin   440      194.0336 kcal/mol        0.4694 kcal/(mol*A)
    xmin   450      193.9358 kcal/mol        0.2172 kcal/(mol*A)
    xmin   460      193.8557 kcal/mol        0.1856 kcal/(mol*A)
    xmin   470      193.8071 kcal/mol        0.2121 kcal/(mol*A)
    xmin   480      193.7464 kcal/mol        0.3667 kcal/(mol*A)
    xmin   490      193.7024 kcal/mol        0.1903 kcal/(mol*A)
    xmin   500      193.6415 kcal/mol        0.3645 kcal/(mol*A)
    xmin   510      193.5785 kcal/mol        0.2654 kcal/(mol*A)
    xmin   520      193.5355 kcal/mol        0.3164 kcal/(mol*A)
    xmin   530      193.4653 kcal/mol        0.1666 kcal/(mol*A)
    xmin   540      193.4334 kcal/mol        0.2079 kcal/(mol*A)
    xmin   550      193.3802 kcal/mol        0.2535 kcal/(mol*A)
    xmin   560      193.3507 kcal/mol        0.1663 kcal/(mol*A)
    xmin   570      193.2777 kcal/mol        0.5671 kcal/(mol*A)
    xmin   580      193.2399 kcal/mol        0.2445 kcal/(mol*A)
    xmin   590      193.2152 kcal/mol        0.1669 kcal/(mol*A)
    xmin   600      193.1698 kcal/mol        0.1541 kcal/(mol*A)
    xmin   610      193.1445 kcal/mol        0.2675 kcal/(mol*A)
    xmin   620      193.0573 kcal/mol        0.4257 kcal/(mol*A)
    xmin   630      192.9692 kcal/mol        0.2645 kcal/(mol*A)
    xmin   640      192.9197 kcal/mol        0.2635 kcal/(mol*A)
    xmin   650      192.8337 kcal/mol        0.2283 kcal/(mol*A)
    xmin   660      192.7806 kcal/mol        0.3345 kcal/(mol*A)
    xmin   670      192.6936 kcal/mol        0.3329 kcal/(mol*A)
    xmin   680      192.6168 kcal/mol        0.3170 kcal/(mol*A)
    xmin   690      192.5765 kcal/mol        0.1580 kcal/(mol*A)
    xmin   700      192.5359 kcal/mol        0.3819 kcal/(mol*A)
    xmin   710      192.4607 kcal/mol        0.1619 kcal/(mol*A)
    xmin   720      192.4032 kcal/mol        0.4018 kcal/(mol*A)
    xmin   730      192.3386 kcal/mol        0.3892 kcal/(mol*A)
    xmin   740      192.2814 kcal/mol        0.1515 kcal/(mol*A)
    xmin   750      192.2283 kcal/mol        0.2742 kcal/(mol*A)
    xmin   760      192.1651 kcal/mol        0.2549 kcal/(mol*A)
    xmin   770      192.1000 kcal/mol        0.3505 kcal/(mol*A)
    xmin   780      192.0478 kcal/mol        0.3171 kcal/(mol*A)
    xmin   790      191.9854 kcal/mol        0.3192 kcal/(mol*A)
    xmin   800      191.9379 kcal/mol        0.2073 kcal/(mol*A)
    xmin   810      191.8944 kcal/mol        0.4580 kcal/(mol*A)
    xmin   820      191.8105 kcal/mol        0.2531 kcal/(mol*A)
    xmin   830      191.6070 kcal/mol        0.3260 kcal/(mol*A)
    xmin   840      191.5356 kcal/mol        0.3652 kcal/(mol*A)
    xmin   850      191.4513 kcal/mol        0.1328 kcal/(mol*A)
    xmin   860      191.3767 kcal/mol        0.3445 kcal/(mol*A)
    xmin   870      191.3244 kcal/mol        0.3275 kcal/(mol*A)
    xmin   880      191.2224 kcal/mol        0.3053 kcal/(mol*A)
    xmin   890      191.1456 kcal/mol        0.6373 kcal/(mol*A)
    xmin   900      191.0628 kcal/mol        0.2590 kcal/(mol*A)
    xmin   910      191.0334 kcal/mol        0.1410 kcal/(mol*A)
    xmin   920      191.0177 kcal/mol        0.1454 kcal/(mol*A)
    xmin   930      191.0032 kcal/mol        0.1475 kcal/(mol*A)
    xmin   940      190.9896 kcal/mol        0.1472 kcal/(mol*A)
    xmin   950      190.9767 kcal/mol        0.1460 kcal/(mol*A)
    xmin   960      190.9649 kcal/mol        0.1400 kcal/(mol*A)
    xmin   970      190.9542 kcal/mol        0.1320 kcal/(mol*A)
    xmin   980      190.9447 kcal/mol        0.1272 kcal/(mol*A)
    xmin   990      190.9362 kcal/mol        0.1192 kcal/(mol*A)
    xmin  1000      190.9285 kcal/mol        0.1181 kcal/(mol*A)
    xmin  1010      190.9212 kcal/mol        0.1181 kcal/(mol*A)
    xmin  1020      190.9142 kcal/mol        0.1128 kcal/(mol*A)
    xmin  1030      190.9078 kcal/mol        0.1082 kcal/(mol*A)
    xmin  1040      190.9018 kcal/mol        0.1087 kcal/(mol*A)
    xmin  1050      190.8963 kcal/mol        0.1031 kcal/(mol*A)
    xmin  1060      190.8914 kcal/mol        0.0886 kcal/(mol*A)
    xmin  1070      190.8877 kcal/mol        0.0836 kcal/(mol*A)
    xmin  1080      190.8842 kcal/mol        0.0817 kcal/(mol*A)
    xmin  1090      190.8808 kcal/mol        0.0820 kcal/(mol*A)
    xmin  1100      190.8773 kcal/mol        0.0834 kcal/(mol*A)
    xmin  1110      190.8738 kcal/mol        0.0852 kcal/(mol*A)
    xmin  1120      190.8697 kcal/mol        0.1160 kcal/(mol*A)
    xmin  1130      190.8665 kcal/mol        0.0385 kcal/(mol*A)
    xmin  1140      190.8625 kcal/mol        0.0496 kcal/(mol*A)
    xmin  1150      190.8610 kcal/mol        0.0521 kcal/(mol*A)
    xmin  1160      190.8595 kcal/mol        0.0602 kcal/(mol*A)
    xmin  1170      190.8573 kcal/mol        0.0785 kcal/(mol*A)
    xmin  1180      190.8538 kcal/mol        0.2014 kcal/(mol*A)
    xmin  1190      190.8465 kcal/mol        0.0925 kcal/(mol*A)
    xmin  1200      190.8419 kcal/mol        0.0886 kcal/(mol*A)
    xmin  1210      190.8374 kcal/mol        0.1091 kcal/(mol*A)
    xmin  1220      190.8319 kcal/mol        0.0758 kcal/(mol*A)
    xmin  1230      190.8263 kcal/mol        0.1151 kcal/(mol*A)
    

  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\tool.py", line 263, in add_charges  
add_nonstandard_res_charges(self.session, residues, charge, method=method)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 319, in
add_nonstandard_res_charges  
nonstd_charge(session, tautomer_residues, net_charge, method, status=status)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 602, in nonstd_charge  
raise ChargeError(ante_failure_msg)  
chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for
residue HEM[non-FE]  
Check reply log for details  
  
chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for
residue HEM[non-FE]  
Check reply log for details  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 602, in nonstd_charge  
raise ChargeError(ante_failure_msg)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 Core Profile Context 23.11.1.231020
OpenGL renderer: AMD Radeon RX 6750 XT
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: pt_BR.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: ASUS
Model: System Product Name
OS: Microsoft Windows 10 Pro (Build 19045)
Memory: 34,265,829,376
MaxProcessMemory: 137,438,953,344
CPU: 12 AMD Ryzen 5 5600 6-Core Processor              
OSLanguage: pt-BR

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    comtypes: 1.1.14
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pywin32: 305
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    WMI: 1.5.1
    zipp: 3.15.0