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Electrostatics / pdb2pqr

PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.
http://www.poissonboltzmann.org/
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server stuck #318

Closed sunimei3 closed 2 years ago

sunimei3 commented 2 years ago

Hi Is PDB2PQR server stuck or just the queue is very long suddenly?

sobolevnrm commented 2 years ago

Hello. I just tried a calculation and it worked without issue. Can you please try again and/or post more information about the specific calculation that failed for you?

sunimei3 commented 2 years ago

https://server.poissonboltzmann.org/jobstatus?jobtype=pdb2pqr&jobid=k9pf3zbqi6&date=2022-05-26

sunimei3 commented 2 years ago

I see, it seems to be input-dependent. It hangs there if I use a certain input. I will look at the file I submited

sunimei3 commented 2 years ago

https://server.poissonboltzmann.org/jobstatus?jobtype=pdb2pqr&jobid=edfrkmxem7&date=2022-05-27 Could you please inform us what does this error mean?

2022-05-27 16:10:09,844 WARNING:main.py:664:non_trivial:Using ZAP9 forcefield for ligand radii. 2022-05-27 16:10:09,846 WARNING:main.py:692:non_trivial:Residue ILD A 201 has non-integer charge: 103.5 deviates by 0.5 from integral, exceeding error tolerance 0.001 2022-05-27 16:10:09,846 CRITICAL:main.py:793:main_driver:103.5 deviates by 0.5 from integral, exceeding error tolerance 0.001 2022-05-27 16:10:09,846 CRITICAL:main.py:794:main_driver:Giving up.

sobolevnrm commented 2 years ago

There is a problem with the charge assignment routine on your input file. Does it have unusual atoms in it?

GeorgianaLiang commented 2 years ago

Is there any specific way to tweak the input to enable the job to run faster (with shorter pending time)?

jbardhan commented 2 years ago

Hello!

Is this last question (about enabling the job to run faster) about the same inputs/problems used in the original question that opened this issue? Just checking if we should open a new ticket.

Thanks, Jay

GeorgianaLiang commented 2 years ago

Thank you so much for the email! The problem was solved. Thanks, Georgiana

发件人: Jaydeep Bardhan @.> 发送时间: 2022年6月24日 16:24 收件人: Electrostatics/pdb2pqr @.> 抄送: GeorgianaLiang @.>; Comment @.> 主题: Re: [Electrostatics/pdb2pqr] server stuck (Issue #318)

Hello!

Is this last question (about enabling the job to run faster) about the same inputs/problems used in the original question that opened this issue? Just checking if we should open a new ticket.

Thanks, Jay

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