Add Charge failure

[haniehtanhaeiana@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19042
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\HYPER-STOCK-TABRIZ\Desktop\cancer\8a8z.pdb format pdb

8a8z.pdb title:  
Crystal structure of danio rerio HDAC6 CD2 In complex with In situ
enzymatically hydrolyzed DFMO-based ITF5924 [more info...]  
  
Chain information for 8a8z.pdb #1  
---  
Chain | Description | UniProt  
A B | histone deacetylase 6 | F8W4B7_DANRE 440-798  
  
Non-standard residues in 8a8z.pdb #1  
---  
K — potassium ion  
LDL —
4-[[4-[4-(imidazolidin-2-ylideneamino)phenyl]-1,2,3-triazol-1-yl]methyl]benzohydrazide  
ZN — zinc ion  
  

> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"

5580 atoms, 5722 bonds, 714 residues, 1 model selected  

> ui tool show "Dock Prep"

Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to 8a8z.pdb #1  
---  
notes | Termini for 8a8z.pdb (#1) chain A determined from SEQRES records  
Termini for 8a8z.pdb (#1) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: /A PRO 442, /B PRO 442  
Chain-final residues that are actual C termini: /A ARG 798, /B ARG 798  
Chain-final residues that are not actual C termini:  
785 hydrogen bonds  
5455 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 ZN (net charge +2) with am1-bcc method  
Assigning partial charges to residue K (net charge +1) with am1-bcc method  
Assigning partial charges to residue LDL (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\HYPER-~1\AppData\Local\Temp\tmpardb74ek\ante.in.mol2 -fi mol2 -o
C:\Users\HYPER-~1\AppData\Local\Temp\tmpardb74ek\ante.out.mol2 -fo mol2 -c bcc
-nc -1 -j 5 -s 2 -dr n  
(LDL) ``  
(LDL) `Welcome to antechamber 20.0: molecular input file processor.`  
(LDL) ``  
(LDL) `Info: Finished reading file
(C:\Users\HYPER-~1\AppData\Local\Temp\tmpardb74ek\ante.in.mol2); atoms read
(45), bonds read (48).`  
(LDL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(LDL) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(LDL) `bash.exe: warning: could not find /tmp, please create!`  
(LDL) ``  
(LDL) ``  
(LDL) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(LDL) `bash.exe: warning: could not find /tmp, please create!`  
(LDL) `Info: Total number of electrons: 196; net charge: -1`  
(LDL) ``  
(LDL) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`  
(LDL) `bash.exe: warning: could not find /tmp, please create!`  
(LDL) `/usr/bin/antechamber: Fatal Error!`  
(LDL) `Unable to find sqm charges in file (sqm.out).`  
(LDL) `Verify the filename and the file contents.`  
  
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 = 70
    
    | QMMM: *** Selected Hamiltonian *** 
    | QMMM: AM1         
    
    | QMMM: *** Parameter sets in use ***
    | QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    | 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: 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 =      129
    | QMMM:    diag iterations used for timing =       10
    | QMMM:
    | QMMM:              Internal diag routine = 0.060927 seconds
    | QMMM:                 Dspev diag routine = 0.056343 seconds
    | QMMM:                Dspevd diag routine = 0.042435 seconds
    | QMMM:                Dspevx diag routine = 0.203451 seconds
    | QMMM:                 Dsyev diag routine = 0.062155 seconds
    | QMMM:                Dsyevd diag routine = 0.048793 seconds
    | QMMM:                Dsyevr diag routine = 0.054935 seconds
    | QMMM:
    | QMMM:                Pseudo diag routine = 0.027087 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      N      -11.4500   -9.1240   -4.4640
      QMMM:     2        2      N      -12.3670   -9.6200   -6.3520
      QMMM:     3        3      C       -7.7850  -11.2780   -4.4120
      QMMM:     4        4      C       -8.7870  -10.3320   -4.5620
      QMMM:     5        5      C       -9.2440   -9.5820   -3.4910
      QMMM:     6        6      C      -10.3640   -8.5690   -3.6430
      QMMM:     7        7      C      -13.1590  -10.1140   -5.3630
      QMMM:     8        8      C      -14.6100  -11.3970   -6.9310
      QMMM:     9        9      C      -16.6440  -11.4860   -5.0610
      QMMM:    10       10      C      -18.7600  -12.9630   -7.6730
      QMMM:    11       11      C      -19.5980  -12.6310   -9.7810
      QMMM:    12       12      C       -7.1600  -11.4800   -3.1860
      QMMM:    13       13      C       -7.6210  -10.7310   -2.1100
      QMMM:    14       14      C       -8.6510   -9.8100   -2.2610
      QMMM:    15       15      N      -11.3190   -9.0350   -5.8070
      QMMM:    16       16      C      -14.4060  -10.8160   -5.6780
      QMMM:    17       17      C      -15.7950  -12.0460   -7.2360
      QMMM:    18       18      C      -15.4410  -10.8670   -4.7500
      QMMM:    19       19      C      -16.8220  -12.0970   -6.2950
      QMMM:    20       20      N      -18.0590  -12.7600   -6.5180
      QMMM:    21       21      N      -19.8250  -13.7560   -7.7490
      QMMM:    22       22      C      -20.6080  -13.3900   -8.9220
      QMMM:    23       23      N      -18.5090  -12.4060   -8.8400
      QMMM:    24       24      C      -12.5750   -9.8000   -4.1590
      QMMM:    25       25      C       -6.0500  -12.4740   -3.0620
      QMMM:    26       26      N       -5.0790  -12.2240   -2.1740
      QMMM:    27       27      N       -3.9730  -13.1090   -2.0480
      QMMM:    28       28      O       -5.9510  -13.4620   -3.7860
      QMMM:    29       29      H       -7.4840  -11.8700   -5.2640
      QMMM:    30       30      H       -9.2220  -10.1760   -5.5380
      QMMM:    31       31      H       -9.9740   -7.6720   -4.1230
      QMMM:    32       32      H      -10.7530   -8.3110   -2.6580
      QMMM:    33       33      H      -13.8300  -11.3390   -7.6760
      QMMM:    34       34      H      -17.4470  -11.4920   -4.3380
      QMMM:    35       35      H      -19.6720  -12.3370  -10.8180
      QMMM:    36       36      H       -7.1700  -10.8670   -1.1380
      QMMM:    37       37      H       -8.9970   -9.2590   -1.3990
      QMMM:    38       38      H      -15.9230  -12.5120   -8.2020
      QMMM:    39       39      H      -15.3070  -10.4200   -3.7760
      QMMM:    40       40      H      -18.4900  -13.1430   -5.6890
      QMMM:    41       41      H      -21.6460  -13.6030   -9.1320
      QMMM:    42       42      H      -12.9420  -10.0440   -3.1730
      QMMM:    43       43      H       -5.1330  -11.4020   -1.5900
      QMMM:    44       44      H      -20.0540  -14.4930   -7.0980
      QMMM:    45       45      H       -4.2720  -13.9590   -1.5920
    
    --------------------------------------------------------------------------------
      RESULTS
    --------------------------------------------------------------------------------
    
          iter         sqm energy              rms gradient
          ----    -------------------    -----------------------
    xmin    10      205.4714 kcal/mol        1.4681 kcal/(mol*A)
    xmin    20      203.8836 kcal/mol        0.3789 kcal/(mol*A)
    xmin    30      203.5776 kcal/mol        0.8732 kcal/(mol*A)
    xmin    40      203.3251 kcal/mol        0.6408 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 LDL  
Check reply log for details  
  
chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for
residue LDL  
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.  
  

Failed to send bug report. Bug report server www.rbvi.ucsf.edu is unavailable  




OpenGL version: 3.3.148201 Core Profile Forward-Compatible Context 20.50.02.01 27.20.15002.1004
OpenGL renderer: AMD Radeon(TM) Graphics
OpenGL vendor: ATI Technologies Inc.

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

Manufacturer: HP
Model: HP Pavilion Laptop 15-eh1xxx
OS: Microsoft Windows 10 Pro (Build 19042)
Memory: 7,886,143,488
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 5700U with Radeon Graphics         
OSLanguage: en-US

Installed Packages:
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    appdirs: 1.4.4
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    ChimeraX-AddH: 2.2.5
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