Pending job start

Question

Pending job start

Opened this issue 2 years ago · 4 comments

I am trying to get the predicted PKa for an enzyme and some variants. The modifications to the enzyme has been conducted using Pymol and the the PDB file was extracted. When I upload the PDB files, the server gets stuck at “pending job start” for hours without giving me any results.

Answer 1 · 2023-04-17T00:35:22.000Z

Hello --

As I mentioned in jensengroup/propka#162, I am not able to reproduce this error using the 1FAS PDB. I need more information about the problem; ideally, the PDB file you're using for the upload.

Thank you

Answer 2 · 2023-04-17T00:48:23.000Z

Hello Nathan, As I mentioned the PDB file I’m using is available on my laptop and the application PyMol was used to create it. For example, I made a variant by mutating the His40 amino acid to an alanine. Attached is the PDB file for that, and below is the link that takes you to the job status where you are able to see that it’s been running for quite some time. Another one is the PDB file for the FGD enzyme (F420 dependent glucose-6-phosphate dehydrogenase) without the citrate molecule. I also made this PDB file using PyMol, and the second link will take you to the job status. I hope this information is enough, if you need more information please let me know! https://server.poissonboltzmann.org/jobstatus?jobtype=pdb2pqr&jobid=19e8thj9uu&date=2023-04-14 https://server.poissonboltzmann.org/jobstatus?jobtype=pdb2pqr&jobid=c2xc7t6mo7&date=2023-04-14 Regards, Alaa Aziz Teaching Assistant Department of Chemistry and Biochemistry University of Texas at Arlington 700 Planetarium Place Arlington, Texas 76019-0065 From: Nathan Baker ***@***.***> Date: Sunday, April 16, 2023 at 7:35 PM To: Electrostatics/pdb2pqr ***@***.***> Cc: Aziz, Alaa ***@***.***>, Author ***@***.***> Subject: Re: [Electrostatics/pdb2pqr] Pending job start (Issue #357) [External] Hello -- As I mentioned in jensengroup/propka#162<jensengroup/propka#162>, I am not able to reproduce this error using the 1FAS PDB. I need more information about the problem; ideally, the PDB file you're using for the upload. Thank you — Reply to this email directly, view it on GitHub<#357 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A7FKIHRYNI4NWOZFXUV2HN3XBSF5JANCNFSM6AAAAAAXAL5RHU>. You are receiving this because you authored the thread.Message ID: ***@***.***>

Answer 3 · 2023-04-17T03:36:52.000Z

Hi @axm8099 --

I can't troubleshoot this because I can't see the input PDB files. I'm adding @Eo300 to see if he can debug from his side.

Thanks,

Nathan

Answer 4 · 2023-04-17T18:32:15.000Z

Dear Nathan, The issue was with the naming of my PDB file. I was able to get the results by simply changing the name of the file to the 4 pdb ID code. Your continuous assistance was very much appreciated! Regards, Alaa Aziz Teaching Assistant Department of Chemistry and Biochemistry University of Texas at Arlington 700 Planetarium Place Arlington, Texas 76019-0065 From: Nathan Baker ***@***.***> Date: Sunday, April 16, 2023 at 10:37 PM To: Electrostatics/pdb2pqr ***@***.***> Cc: Aziz, Alaa ***@***.***>, Mention ***@***.***> Subject: Re: [Electrostatics/pdb2pqr] Pending job start (Issue #357) [External] Hi @axm8099<https://github.com/axm8099> -- I can't troubleshoot this because I can't see the input PDB files. I'm adding @Eo300<https://github.com/Eo300> to see if he can debug from his side. Thanks, Nathan — Reply to this email directly, view it on GitHub<#357 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A7FKIHW6ADDFYUDWGZY4JK3XBS3F5ANCNFSM6AAAAAAXAL5RHU>. You are receiving this because you were mentioned.Message ID: ***@***.***>