Add Charge: boron

[nishaofficial19@…]

The following bug report has been submitted:
Platform:        Linux-6.8.0-59-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
unablle to doc prep 

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /home/hp/Desktop/NIsha/ST.Xavier/Final_Project/GSE248260/Docking/bortezomib_3D.pdb

> ui tool show "Add Hydrogens"

> addh

Summary of feedback from adding hydrogens to bortezomib_3D.pdb #1  
---  
warning | Unknown hybridization for atom (B) of residue type UNL; not adding
hydrogens to it  
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:  
0 hydrogen bonds  
0 hydrogens added  
  

> ui tool show "Add Charges"

Closest equivalent command: addcharge & sel standardizeResidues
5BU,CSL,MSE,UMS  
Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue UNL (net charge +0) with am1-bcc method  

Atom whose IDATM type has no equivalent Sybyl type: /? UNL 1 B1 (type: B)  

Running ANTECHAMBER command: /usr/lib/ucsf-
chimerax/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
/tmp/tmpdbab76y4/ante.in.mol2 -fi mol2 -o /tmp/tmpdbab76y4/ante.out.mol2 -fo
mol2 -c bcc -nc 0 -j 5 -s 2 -dr n  
(UNL) ``  
(UNL) `Welcome to antechamber 20.0: molecular input file processor.`  
(UNL) ``  
(UNL) `Info: Finished reading file (/tmp/tmpdbab76y4/ante.in.mol2); atoms read
(53), bonds read (54).`  
(UNL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(UNL) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(UNL) `Warning: For atom (ID: 28, Name: B1) the best APS is not zero.`  
(UNL) ` Bonds involving this atom are frozen.`  
(UNL) ``  
(UNL) ``  
(UNL) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(UNL) `Info: Total number of electrons: 204; net charge: 0`  
(UNL) ``  
(UNL) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out`  
(UNL) `/usr/lib/ucsf-chimerax/bin/amber20/bin/antechamber: Fatal Error!`  
(UNL) `Cannot properly run "/usr/lib/ucsf-chimerax/bin/amber20/bin/sqm -O -i
sqm.in -o sqm.out".`  
  
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: Atom number:     28 has atomic number    5.
    QMMM: There are no AM1 parameters for this element. Sorry.
     SANDER BOMB in subroutine qm2_load_params_and_allocate
     UNSUPPORTED ELEMENT
     QM AM1 NOT AVAILABLE FOR THIS ATOM
    

  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/add_charge/tool.py", line 263, in add_charges  
add_nonstandard_res_charges(self.session, residues, charge, method=method)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/add_charge/charge.py", line 330, in
add_nonstandard_res_charges  
nonstd_charge(session, tautomer_residues, net_charge, method, status=status)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/add_charge/charge.py", line 634, in nonstd_charge  
raise ChargeError(ante_failure_msg)  
chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for
residue UNL  
Check reply log for details  
  
chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for
residue UNL  
Check reply log for details  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/add_charge/charge.py", line 634, in nonstd_charge  
raise ChargeError(ante_failure_msg)  
  
See log for complete Python traceback.  
  

> select ::name="UNL"

53 atoms, 54 bonds, 1 residue, 1 model selected  

> save
> /home/hp/Desktop/NIsha/ST.Xavier/Final_Project/GSE248260/Docking/bortezomib_cleaned.pdb
> relModel #1

> save
> /home/hp/Desktop/NIsha/ST.Xavier/Final_Project/GSE248260/Docking/borte.pdb
> selectedOnly true relModel #1

> select clear

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to bortezomib_3D.pdb #1  
---  
warning | Unknown hybridization for atom (B) of residue type UNL; not adding
hydrogens to it  
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:  
0 hydrogen bonds  
0 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 UNL (net charge +0) with gasteiger method  

Atom whose IDATM type has no equivalent Sybyl type: /? UNL 1 B1 (type: B)  

Running ANTECHAMBER command: /usr/lib/ucsf-
chimerax/bin/amber20/bin/antechamber -i /tmp/tmpzst608jf/ante.in.mol2 -fi mol2
-o /tmp/tmpzst608jf/ante.out.mol2 -fo mol2 -c gas -nc 0 -j 5 -s 2 -dr n  
(UNL) ``  
(UNL) `Welcome to antechamber 20.0: molecular input file processor.`  
(UNL) ``  
(UNL) `Info: Finished reading file (/tmp/tmpzst608jf/ante.in.mol2); atoms read
(53), bonds read (54).`  
(UNL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(UNL) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(UNL) `Warning: For atom (ID: 28, Name: B1) the best APS is not zero.`  
(UNL) ` Bonds involving this atom are frozen.`  
(UNL) ``  
(UNL) ``  
(UNL) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(UNL) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/atomtype -i
ANTECHAMBER_GAS.AC -o ANTECHAMBER_GAS_AT.AC -d /usr/lib/ucsf-
chimerax/bin/amber20/dat/antechamber/ATOMTYPE_GAS.DEF`  
(UNL) `/usr/lib/ucsf-chimerax/bin/amber20/bin/antechamber: Fatal Error!`  
(UNL) `No Gasteiger parameter for atom (ID: 27, Name: B1, Type: DU).`  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/add_charge/tool.py", line 263, in add_charges  
add_nonstandard_res_charges(self.session, residues, charge, method=method)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/add_charge/charge.py", line 330, in
add_nonstandard_res_charges  
nonstd_charge(session, tautomer_residues, net_charge, method, status=status)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/add_charge/charge.py", line 634, in nonstd_charge  
raise ChargeError(ante_failure_msg)  
chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for
residue UNL  
Check reply log for details  
  
chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for
residue UNL  
Check reply log for details  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/add_charge/charge.py", line 634, in nonstd_charge  
raise ChargeError(ante_failure_msg)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.6 (Core Profile) Mesa 23.2.1-1ubuntu3.1~22.04.3
OpenGL renderer: Mesa Intel(R) UHD Graphics 620 (KBL GT2)
OpenGL vendor: Intel

Python: 3.11.2
Locale: en_IN.ISO8859-1
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb

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[Eric Pettersen]

Hi Nisha,

The underlying AMBER program that Add Charge uses (Antechamber) cannot handle boron, and therefore ChimeraX cannot assign charges to compounds containing boron.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab