a error about antecamber

[kingljy0818]

A error was prompted in the following:

2022-09-08 11:27:09,197: Setting CUDA platform to use precision model 'mixed'.
2022-09-08 11:27:09,319: Single node: executing <function ExperimentBuilder._check_resume at 0x7fbfc14a4c20>
2022-09-08 11:27:09,320: Running _setup_molecules serially.
Traceback (most recent call last):
File "/home/anaconda3/bin/yank", line 10, in
sys.exit(main())
File "/home/anaconda3/lib/python3.7/site-packages/yank/cli.py", line 73, in main
dispatched = getattr(commands, command).dispatch(command_args)
File "/home/anaconda3/lib/python3.7/site-packages/yank/commands/script.py", line 155, in dispatch
yaml_builder.run_experiments(write_status=write_status)
File "/home/anaconda3/lib/python3.7/site-packages/yank/experiment.py", line 737, in run_experiments
self._setup_experiments()
File "/home/anaconda3/lib/python3.7/site-packages/yank/experiment.py", line 2325, in _setup_experiments
self._db.setup_all_systems()
File "/home/anaconda3/lib/python3.7/site-packages/yank/pipeline.py", line 1385, in setup_all_systems
send_results_to=None, group_size=1, sync_nodes=True)
File "/home/anaconda3/lib/python3.7/site-packages/mpiplus/mpiplus.py", line 512, in distribute
all_results = [task(job_args, *other_args, **kwargs) for job_args in distributed_args]
File "/home/anaconda3/lib/python3.7/site-packages/mpiplus/mpiplus.py", line 512, in
all_results = [task(job_args, *other_args, **kwargs) for job_args in distributed_args]
File "/home/anaconda3/lib/python3.7/site-packages/yank/pipeline.py", line 1697, in _setup_molecules
gaff_version=gaff)
File "/home/anaconda3/lib/python3.7/site-packages/openmoltools/amber.py", line 372, in run_antechamber
raise Exception(msg)
Exception: antechamber failed to produce output mol2 file
command: antechamber -i in.mol2 -fi mol2 -o out.mol2 -fo mol2 -s 2 -at gaff -c bcc
output:

Running: /home/anaconda3/bin/../bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac

Running: /home/anaconda3/bin/../bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Total number of electrons: 241; net charge: 0
INFO: Number of electrons is odd: 241
Please check the total charge (-nc flag) and spin multiplicity (-m flag)

Running: /home/anaconda3/bin/../bin/sqm -O -i sqm.in -o sqm.out
Error: cannot run "/home/anaconda3/bin/../bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit--------------------------------------------------------------------------------
input mol2:

Molecule written by the XED library from Cresset

@MOLECULE
ID7_4_PQ1:1|PQ1-4_Forge_Aligned_ID7_4_Charge_Modified|sdf|1|dock1
57 62 1
SMALL
USER_CHARGES
@ATOM
...

---

Could you help me to solve the error in the above. Many thanks.

[jslim-furame]

Total number of electrons: 241; net charge: 0
INFO: Number of electrons is odd: 241

The error occurs because the number of electrons is odd. Please check the charge of your ligand or the protonation states. Run the antechamber in your local computer and verify what is the problem. Consider adding hydrogens using Chimera or other well-known tools like Maestro. If the charge is wrong, specify "-nc" flag in your YANK yaml file.

[kingljy0818]

Thank you for your response. I have checked the charge of the ligand with a positive charge, and added the netcharge = 1 in my YANK yaml file, but I got another error in the following:

Traceback (most recent call last):
File "/home/anaconda3/bin/yank", line 10, in
sys.exit(main())
File "/home/anaconda3/lib/python3.7/site-packages/yank/cli.py", line 73, in main
dispatched = getattr(commands, command).dispatch(command_args)
File "/home/anaconda3/lib/python3.7/site-packages/yank/commands/script.py", line 147, in dispatch
yaml_builder = ExperimentBuilder(script=yaml_path, job_id=job_id, n_jobs=n_jobs)
File "/home/anaconda3/lib/python3.7/site-packages/yank/experiment.py", line 591, in init
self.parse(script)
File "/home/anaconda3/lib/python3.7/site-packages/yank/experiment.py", line 646, in parse
yaml_content = yaml.load(f, Loader=YankLoader)
File "/home/anaconda3/lib/python3.7/site-packages/yaml/init.py", line 114, in load
return loader.get_single_data()
File "/home/anaconda3/lib/python3.7/site-packages/yaml/constructor.py", line 49, in get_single_data
node = self.get_single_node()
File "/home/anaconda3/lib/python3.7/site-packages/yaml/composer.py", line 36, in get_single_node
document = self.compose_document()
File "/home/anaconda3/lib/python3.7/site-packages/yaml/composer.py", line 55, in compose_document
node = self.compose_node(None, None)
File "/home/anaconda3/lib/python3.7/site-packages/yaml/composer.py", line 84, in compose_node
node = self.compose_mapping_node(anchor)
File "/home/anaconda3/lib/python3.7/site-packages/yaml/composer.py", line 133, in compose_mapping_node
item_value = self.compose_node(node, item_key)
File "/home/anaconda3/lib/python3.7/site-packages/yaml/composer.py", line 84, in compose_node
node = self.compose_mapping_node(anchor)
File "/home/anaconda3/lib/python3.7/site-packages/yaml/composer.py", line 133, in compose_mapping_node
item_value = self.compose_node(node, item_key)
File "/home/anaconda3/lib/python3.7/site-packages/yaml/composer.py", line 84, in compose_node
node = self.compose_mapping_node(anchor)
File "/home/anaconda3/lib/python3.7/site-packages/yaml/composer.py", line 133, in compose_mapping_node
item_value = self.compose_node(node, item_key)
File "/home/anaconda3/lib/python3.7/site-packages/yaml/composer.py", line 84, in compose_node
node = self.compose_mapping_node(anchor)
File "/home/anaconda3/lib/python3.7/site-packages/yaml/composer.py", line 127, in compose_mapping_node
while not self.check_event(MappingEndEvent):
File "/home/anaconda3/lib/python3.7/site-packages/yaml/parser.py", line 98, in check_event
self.current_event = self.state()
File "/home/anaconda3/lib/python3.7/site-packages/yaml/parser.py", line 428, in parse_block_mapping_key
if self.check_token(KeyToken):
File "/home/anaconda3/lib/python3.7/site-packages/yaml/scanner.py", line 115, in check_token
while self.need_more_tokens():
File "/home/anaconda3/lib/python3.7/site-packages/yaml/scanner.py", line 152, in need_more_tokens
self.stale_possible_simple_keys()
File "/home/anaconda3/lib/python3.7/site-packages/yaml/scanner.py", line 292, in stale_possible_simple_keys
"could not find expected ':'", self.get_mark())
yaml.scanner.ScannerError: while scanning a simple key
in "PQ1_P1-3pp0b-explicit.yaml", line 25, column 7
could not find expected ':'
in "PQ1_P1-3pp0b-explicit.yaml", line 27, column 1

---

I still need your help to solve this problem, many thanks.

[andrrizzi]

Hi @kingljy0818. This looks like a simple YAML syntax error in your script. Some extra : character somewhere?

[jslim-furame]

Simply, bcc -nc 1 Its syntax follows antechamber. 2022년 9월 8일 (목) 21:02, kingljy0818 ***@***.***>님이 작성:

…

Thank you for your response. I have checked the charge of the ligand with a positive charge, would ask you how to specify the '-nc' flag in my YANK yaml file? — Reply to this email directly, view it on GitHub <#1289 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AKXZQ6SHMDMUSM3Q662D7W3V5HIVJANCNFSM6AAAAAAQHKKXBA> . You are receiving this because you commented.Message ID: ***@***.***>

[kingljy0818]

Simply, bcc -nc 1 Its syntax follows antechamber. 2022년 9월 8일 (목) 21:02, kingljy0818 @.>님이 작성:
…
Thank you for your response. I have checked the charge of the ligand with a positive charge, would ask you how to specify the '-nc' flag in my YANK yaml file? — Reply to this email directly, view it on GitHub <#1289 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKXZQ6SHMDMUSM3Q662D7W3V5HIVJANCNFSM6AAAAAAQHKKXBA . You are receiving this because you commented.Message ID: @.>

Thank you so much. The error was solved as followed your suggestion.