Mol2 not creating metal-coordination pseudobonds

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19044
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/david/Desktop/chlidea.mol2

Opened chlidea.mol2 containing 1 structures (78 atoms, 86 bonds)  

> dockprep

Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to 2dre.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:  
0 hydrogen bonds  
0 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue CLA (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\david\AppData\Local\Temp\tmpowlr2zy2\ante.in.mol2 -fi mol2 -o
C:\Users\david\AppData\Local\Temp\tmpowlr2zy2\ante.out.mol2 -fo mol2 -c bcc
-nc -1 -j 5 -s 2 -dr n  
(CLA) ``  
(CLA) `Welcome to antechamber 20.0: molecular input file processor.`  
(CLA) ``  
(CLA) `Info: Finished reading file
(C:\Users\david\AppData\Local\Temp\tmpowlr2zy2\ante.in.mol2); atoms read (78),
bonds read (86).`  
(CLA) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(CLA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(CLA) `bash.exe: warning: could not find /tmp, please create!`  
(CLA) `Warning: For atom (ID: 1, Name: Mg1) the best APS is not zero.`  
(CLA) ` Bonds involving this atom are frozen.`  
(CLA) ``  
(CLA) ``  
(CLA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(CLA) `bash.exe: warning: could not find /tmp, please create!`  
(CLA) `Info: Total number of electrons: 324; net charge: -1`  
(CLA) ``  
(CLA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`  
(CLA) `bash.exe: warning: could not find /tmp, please create!`  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\dock_prep\cmd.py", line 133, in dock_prep_cmd  
dock_prep_caller(session, structures, memorization=memorize, nogui=True, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\dock_prep\cmd.py", line 112, in dock_prep_caller  
run_steps(session, state)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\dock_prep\cmd.py", line 124, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\dock_prep\prep.py", line 85, in prep  
callback(session, state)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\dock_prep\cmd.py", line 124, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\addh\dock_prep.py", line 36, in run_for_dock_prep  
callback(session, state)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\dock_prep\cmd.py", line 124, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\dock_prep.py", line 37, in run_for_dock_prep  
cmd_addcharge(session, structures.residues, **active_settings)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\cmd.py", line 31, in cmd_addcharge  
add_charges(session, residues, method=method, status=session.logger.status,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 26, in add_charges  
add_nonstandard_res_charges(session, res_list,
estimate_net_charge(res_list[0].atoms),  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 334, 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 598, in nonstd_charge  
raise ChargeError(ante_failure_msg)  
chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for
residue CLA  
Check reply log for details  
  
chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for
residue CLA  
Check reply log for details  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 598, in nonstd_charge  
raise ChargeError(ante_failure_msg)  
  
See log for complete Python traceback.  
  

> dockprep

Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to 2dre.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:  
0 hydrogen bonds  
0 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue CLA (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\david\AppData\Local\Temp\tmpkv0qbxrq\ante.in.mol2 -fi mol2 -o
C:\Users\david\AppData\Local\Temp\tmpkv0qbxrq\ante.out.mol2 -fo mol2 -c bcc
-nc -1 -j 5 -s 2 -dr n  
(CLA) ``  
(CLA) `Welcome to antechamber 20.0: molecular input file processor.`  
(CLA) ``  
(CLA) `Info: Finished reading file
(C:\Users\david\AppData\Local\Temp\tmpkv0qbxrq\ante.in.mol2); atoms read (78),
bonds read (86).`  
(CLA) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(CLA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(CLA) `bash.exe: warning: could not find /tmp, please create!`  
(CLA) `Warning: For atom (ID: 1, Name: Mg1) the best APS is not zero.`  
(CLA) ` Bonds involving this atom are frozen.`  
(CLA) ``  
(CLA) ``  
(CLA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(CLA) `bash.exe: warning: could not find /tmp, please create!`  
(CLA) `Info: Total number of electrons: 324; net charge: -1`  
(CLA) ``  
(CLA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`  
(CLA) `bash.exe: warning: could not find /tmp, please create!`  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\dock_prep\cmd.py", line 133, in dock_prep_cmd  
dock_prep_caller(session, structures, memorization=memorize, nogui=True, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\dock_prep\cmd.py", line 112, in dock_prep_caller  
run_steps(session, state)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\dock_prep\cmd.py", line 124, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\dock_prep\prep.py", line 85, in prep  
callback(session, state)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\dock_prep\cmd.py", line 124, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\addh\dock_prep.py", line 36, in run_for_dock_prep  
callback(session, state)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\dock_prep\cmd.py", line 124, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\dock_prep.py", line 37, in run_for_dock_prep  
cmd_addcharge(session, structures.residues, **active_settings)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\cmd.py", line 31, in cmd_addcharge  
add_charges(session, residues, method=method, status=session.logger.status,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 26, in add_charges  
add_nonstandard_res_charges(session, res_list,
estimate_net_charge(res_list[0].atoms),  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 334, 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 598, in nonstd_charge  
raise ChargeError(ante_failure_msg)  
chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for
residue CLA  
Check reply log for details  
  
chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for
residue CLA  
Check reply log for details  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 598, in nonstd_charge  
raise ChargeError(ante_failure_msg)  
  
See log for complete Python traceback.  
  

> cd "C:/Users/david/Desktop/New folder"

Current working directory is: C:\Users\david\Desktop\New folder  

> dockprep

Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to 2dre.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:  
0 hydrogen bonds  
0 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue CLA (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\david\AppData\Local\Temp\tmpug8p5md6\ante.in.mol2 -fi mol2 -o
C:\Users\david\AppData\Local\Temp\tmpug8p5md6\ante.out.mol2 -fo mol2 -c bcc
-nc -1 -j 5 -s 2 -dr n  
(CLA) ``  
(CLA) `Welcome to antechamber 20.0: molecular input file processor.`  
(CLA) ``  
(CLA) `Info: Finished reading file
(C:\Users\david\AppData\Local\Temp\tmpug8p5md6\ante.in.mol2); atoms read (78),
bonds read (86).`  
(CLA) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(CLA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(CLA) `bash.exe: warning: could not find /tmp, please create!`  
(CLA) `Warning: For atom (ID: 1, Name: Mg1) the best APS is not zero.`  
(CLA) ` Bonds involving this atom are frozen.`  
(CLA) ``  
(CLA) ``  
(CLA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(CLA) `bash.exe: warning: could not find /tmp, please create!`  
(CLA) `Info: Total number of electrons: 324; net charge: -1`  
(CLA) ``  
(CLA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`  
(CLA) `bash.exe: warning: could not find /tmp, please create!`  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\dock_prep\cmd.py", line 133, in dock_prep_cmd  
dock_prep_caller(session, structures, memorization=memorize, nogui=True, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\dock_prep\cmd.py", line 112, in dock_prep_caller  
run_steps(session, state)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\dock_prep\cmd.py", line 124, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\dock_prep\prep.py", line 85, in prep  
callback(session, state)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\dock_prep\cmd.py", line 124, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\addh\dock_prep.py", line 36, in run_for_dock_prep  
callback(session, state)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\dock_prep\cmd.py", line 124, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\dock_prep.py", line 37, in run_for_dock_prep  
cmd_addcharge(session, structures.residues, **active_settings)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\cmd.py", line 31, in cmd_addcharge  
add_charges(session, residues, method=method, status=session.logger.status,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 26, in add_charges  
add_nonstandard_res_charges(session, res_list,
estimate_net_charge(res_list[0].atoms),  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 334, 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 598, in nonstd_charge  
raise ChargeError(ante_failure_msg)  
chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for
residue CLA  
Check reply log for details  
  
chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for
residue CLA  
Check reply log for details  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 598, in nonstd_charge  
raise ChargeError(ante_failure_msg)  
  
See log for complete Python traceback.  
  

> dockprep

Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to 2dre.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:  
0 hydrogen bonds  
0 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue CLA (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\david\AppData\Local\Temp\tmpdxw62nc5\ante.in.mol2 -fi mol2 -o
C:\Users\david\AppData\Local\Temp\tmpdxw62nc5\ante.out.mol2 -fo mol2 -c bcc
-nc -1 -j 5 -s 2 -dr n  
(CLA) ``  
(CLA) `Welcome to antechamber 20.0: molecular input file processor.`  
(CLA) ``  
(CLA) `Info: Finished reading file
(C:\Users\david\AppData\Local\Temp\tmpdxw62nc5\ante.in.mol2); atoms read (78),
bonds read (86).`  
(CLA) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(CLA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(CLA) `bash.exe: warning: could not find /tmp, please create!`  
(CLA) `Warning: For atom (ID: 1, Name: Mg1) the best APS is not zero.`  
(CLA) ` Bonds involving this atom are frozen.`  
(CLA) ``  
(CLA) ``  
(CLA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(CLA) `bash.exe: warning: could not find /tmp, please create!`  
(CLA) `Info: Total number of electrons: 324; net charge: -1`  
(CLA) ``  
(CLA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`  
(CLA) `bash.exe: warning: could not find /tmp, please create!`  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\dock_prep\cmd.py", line 133, in dock_prep_cmd  
dock_prep_caller(session, structures, memorization=memorize, nogui=True, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\dock_prep\cmd.py", line 112, in dock_prep_caller  
run_steps(session, state)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\dock_prep\cmd.py", line 124, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\dock_prep\prep.py", line 85, in prep  
callback(session, state)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\dock_prep\cmd.py", line 124, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\addh\dock_prep.py", line 36, in run_for_dock_prep  
callback(session, state)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\dock_prep\cmd.py", line 124, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\dock_prep.py", line 37, in run_for_dock_prep  
cmd_addcharge(session, structures.residues, **active_settings)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\cmd.py", line 31, in cmd_addcharge  
add_charges(session, residues, method=method, status=session.logger.status,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 26, in add_charges  
add_nonstandard_res_charges(session, res_list,
estimate_net_charge(res_list[0].atoms),  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 334, 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 598, in nonstd_charge  
raise ChargeError(ante_failure_msg)  
chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for
residue CLA  
Check reply log for details  
  
chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for
residue CLA  
Check reply log for details  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 598, in nonstd_charge  
raise ChargeError(ante_failure_msg)  
  
See log for complete Python traceback.  
  

> addcharge charge

Expected a keyword  

> addcharge charge all

Expected a keyword  

> addcharge charge all method am1

Expected a keyword  

> addcharge charge all chargeModel 14SB method am1

Expected a keyword  

> addcharge all chargeModel 14SB method am1

Expected a keyword  

> addcharge all @ chargeModel 14SB method am1

Expected a keyword  

> addcharge all atom chargeModel 14SB method am1

Expected a keyword  

> dockprep

Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to 2dre.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:  
0 hydrogen bonds  
0 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue CLA (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\david\AppData\Local\Temp\tmpwy1cxexh\ante.in.mol2 -fi mol2 -o
C:\Users\david\AppData\Local\Temp\tmpwy1cxexh\ante.out.mol2 -fo mol2 -c bcc
-nc -1 -j 5 -s 2 -dr n  
(CLA) ``  
(CLA) `Welcome to antechamber 20.0: molecular input file processor.`  
(CLA) ``  
(CLA) `Info: Finished reading file
(C:\Users\david\AppData\Local\Temp\tmpwy1cxexh\ante.in.mol2); atoms read (78),
bonds read (86).`  
(CLA) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(CLA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(CLA) `bash.exe: warning: could not find /tmp, please create!`  
(CLA) `Warning: For atom (ID: 1, Name: Mg1) the best APS is not zero.`  
(CLA) ` Bonds involving this atom are frozen.`  
(CLA) ``  
(CLA) ``  
(CLA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(CLA) `bash.exe: warning: could not find /tmp, please create!`  
(CLA) `Info: Total number of electrons: 324; net charge: -1`  
(CLA) ``  
(CLA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`  
(CLA) `bash.exe: warning: could not find /tmp, please create!`  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\dock_prep\cmd.py", line 133, in dock_prep_cmd  
dock_prep_caller(session, structures, memorization=memorize, nogui=True, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\dock_prep\cmd.py", line 112, in dock_prep_caller  
run_steps(session, state)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\dock_prep\cmd.py", line 124, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\dock_prep\prep.py", line 85, in prep  
callback(session, state)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\dock_prep\cmd.py", line 124, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\addh\dock_prep.py", line 36, in run_for_dock_prep  
callback(session, state)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\dock_prep\cmd.py", line 124, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\dock_prep.py", line 37, in run_for_dock_prep  
cmd_addcharge(session, structures.residues, **active_settings)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\cmd.py", line 31, in cmd_addcharge  
add_charges(session, residues, method=method, status=session.logger.status,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 26, in add_charges  
add_nonstandard_res_charges(session, res_list,
estimate_net_charge(res_list[0].atoms),  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 334, 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 598, in nonstd_charge  
raise ChargeError(ante_failure_msg)  
chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for
residue CLA  
Check reply log for details  
  
chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for
residue CLA  
Check reply log for details  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 598, in nonstd_charge  
raise ChargeError(ante_failure_msg)  
  
See log for complete Python traceback.  
  

> dockprep

Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to 2dre.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:  
0 hydrogen bonds  
0 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue CLA (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\david\AppData\Local\Temp\tmptp7ov4yy\ante.in.mol2 -fi mol2 -o
C:\Users\david\AppData\Local\Temp\tmptp7ov4yy\ante.out.mol2 -fo mol2 -c bcc
-nc -1 -j 5 -s 2 -dr n  
(CLA) ``  
(CLA) `Welcome to antechamber 20.0: molecular input file processor.`  
(CLA) ``  
(CLA) `Info: Finished reading file
(C:\Users\david\AppData\Local\Temp\tmptp7ov4yy\ante.in.mol2); atoms read (78),
bonds read (86).`  
(CLA) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(CLA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(CLA) `bash.exe: warning: could not find /tmp, please create!`  
(CLA) `Warning: For atom (ID: 1, Name: Mg1) the best APS is not zero.`  
(CLA) ` Bonds involving this atom are frozen.`  
(CLA) ``  
(CLA) ``  
(CLA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(CLA) `bash.exe: warning: could not find /tmp, please create!`  
(CLA) `Info: Total number of electrons: 324; net charge: -1`  
(CLA) ``  
(CLA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`  
(CLA) `bash.exe: warning: could not find /tmp, please create!`  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\dock_prep\cmd.py", line 133, in dock_prep_cmd  
dock_prep_caller(session, structures, memorization=memorize, nogui=True, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\dock_prep\cmd.py", line 112, in dock_prep_caller  
run_steps(session, state)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\dock_prep\cmd.py", line 124, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\dock_prep\prep.py", line 85, in prep  
callback(session, state)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\dock_prep\cmd.py", line 124, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\addh\dock_prep.py", line 36, in run_for_dock_prep  
callback(session, state)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\dock_prep\cmd.py", line 124, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\dock_prep.py", line 37, in run_for_dock_prep  
cmd_addcharge(session, structures.residues, **active_settings)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\cmd.py", line 31, in cmd_addcharge  
add_charges(session, residues, method=method, status=session.logger.status,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 26, in add_charges  
add_nonstandard_res_charges(session, res_list,
estimate_net_charge(res_list[0].atoms),  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 334, 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 598, in nonstd_charge  
raise ChargeError(ante_failure_msg)  
chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for
residue CLA  
Check reply log for details  
  
chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for
residue CLA  
Check reply log for details  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 598, in nonstd_charge  
raise ChargeError(ante_failure_msg)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 359.00
OpenGL renderer: GeForce GTX 965M/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: Micro-Star International Co., Ltd.
Model: GS60 6QD
OS: Microsoft Windows 10 Home (Build 19044)
Memory: 8,496,087,040
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-6700HQ CPU @ 2.60GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2022.9.24
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    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: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 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: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    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-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    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
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    comtypes: 1.1.10
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.1.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.33
    psutil: 5.9.1
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.6
    pywin32: 303
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    WMI: 1.5.1
    zipp: 3.11.0