Pending job start

[axm8099]

I am trying to run PROPKA calculations on a protein using a pdb file upload but the server is stuck on pending job start. It stays loading for hours without getting results. However when I use the pdb file code it runs the results in 33 seconds. The reason why I need to use the file upload is because I need to do manipulation to the enzyme using pymol and export the pdb file from pymol

[sobolevnrm]

Can you please provide the URL of the server you used?

[axm8099]

Hello Nathan,

I used this link https://server.poissonboltzmann.org/pdb2pqr

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: Saturday, April 15, 2023 at 9:25 PM To: jensengroup/propka @.> Cc: Aziz, Alaa @.>, Author @.> Subject: Re: [jensengroup/propka] Pending job start (Issue #162)

[External]

Can you please provide the URL of the server you used?

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[sobolevnrm]

This is a PDB2PQR issue, not a PROPKA one. Unfortunately, I cannot transfer this issue between organizations.

However, I was unable to reproduce this issue by downloading and re-uploading the 1FAS PDB entry to the server. If you continue to have this problem, can you please repost in the PDB2PQR issues with more information about how to reproduce the issue?

[axm8099]

Hello Nathan,

How do I use the PROPKA server then? I am trying to have predicted PKa values for my enzyme and some variants. Your help is much appreciated

Regards,

Alaa Aziz Graduate Teacher Assistant Department of chemistry and biochemistry University of Texas at Arlington 700 Planetarium Place Arlington, Texas 76019-0065

On Apr 16, 2023, at 10:20, Nathan Baker @.***> wrote:



[External]

Closed #162https://github.com/jensengroup/propka/issues/162 as completed.

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[sobolevnrm]

The PDB2PQR server implements PROPKA; you can perform your pKa calculations there.