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Electrostatics / apbs-pdb2pqr

APBS - software for biomolecular electrostatics and solvation
http://www.poissonboltzmann.org/
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NotImplementedError: PDB2PKA not implemented. #615

Closed arikat closed 4 years ago

arikat commented 4 years ago

Unsure why this error continuously pops up. After general installation of the program, I run the command:

python3 pdb2pqr.py --ff PARSE --titration-state-method pdb2pka --pdb2pka-out temp/ /home/user/Desktop/tidy.pdb /home/user/Desktop/PDB2PQR/out_files/output.pqr

The following error appears (log file attached). Unsure why this is the case. Any help would be appreciated. txt.txt

sobolevnrm commented 4 years ago

Hi --

This is the intended behavior for the current master. Please use one of our releases (and associated tagged branches) instead: https://github.com/Electrostatics/apbs-pdb2pqr/releases

Thank you,

Nathan

arikat commented 4 years ago

I tried some of the other releases. However, they all appear to provide the same error. Is there a specific release you'd recommend? One of the recommendations in the code was to just use pka.py as a standalone script, but it has a number of dependencies in the release, and many of its imports no longer function properly. The read_pdb definition is no longer in pdb.py, for example, it's in input_output.py/. Many other dependencies behave similarly. Should I be changing the imports to make it function properly?

sobolevnrm commented 4 years ago

This release should work as expected: https://github.com/Electrostatics/apbs-pdb2pqr/releases/tag/vPDB2PQR-2.1.1

We're actively working to fix the issues you described in the current release -- that's why we've disabled PDB2PQR in the master branch. There was a lot of redundant and malfunctioning code that we are trying to clean up.

kozlac commented 4 years ago

What python version are you using? You should use python 2.7 for releases <= 2.1.1.

arikat commented 4 years ago

I have both, but Python 2.7 is what I'm using for those releases.

Aarya Venkat

Biochemistry PhD Student, Kannan Lab

Future Faculty Fellow

University of Georgia

https://arikat.github.io/

From: Juan notifications@github.com Sent: Thursday, June 25, 2020 10:41 AM To: Electrostatics/apbs-pdb2pqr apbs-pdb2pqr@noreply.github.com Cc: Aarya Venkat aarya@uga.edu; Author author@noreply.github.com Subject: Re: [Electrostatics/apbs-pdb2pqr] NotImplementedError: PDB2PKA not implemented. (#615)

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

What python version are you using? You should use python 2.7 for releases <= 2.1.1.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Electrostatics/apbs-pdb2pqr/issues/615#issuecomment-649593114, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AKIZAOZ43J7AFWWZJTS7VETRYNO3JANCNFSM4OHQMFAA.

kozlac commented 4 years ago

@arikat If you are still seeing that error, can you provide is with OS, python version, which distribution (e.g. apbs-pdb2pqr-vPDB2PQR-2.1.1-release.tar.gz, apbs-pdb2pqr-vPDB2PQR-2.1.1-release.zip, etc.), how are you invoking pdb2pqr from the command line, and if possible the pdf file as well? Thanks!

arikat commented 4 years ago

I used apbs-pdb2pqr-vPDB2PQR-2.1.1-release.tar.gz.

OS: Ubuntu 18

Python: 2.7

PDB: 1T8L (which we removed extraneous details like Remarks from)

Command line: python3 pdb2pqr.py --ff PARSE --titration-state-method pdb2pka --pdb2pka-out temp/ /home/user/Desktop/tidy.pdb /home/user/Desktop/PDB2PQR/out_files/output.pqr

Specifically we're trying to use the pdb2pka method. The regular pdb2pqr method works fine.

Thank you for helping!

Kind regards, Aarya

Aarya Venkat

Biochemistry PhD Student, Kannan Lab

Future Faculty Fellow

University of Georgia

https://arikat.github.io/

From: Juan notifications@github.com Sent: Thursday, June 25, 2020 10:56 AM To: Electrostatics/apbs-pdb2pqr apbs-pdb2pqr@noreply.github.com Cc: Aarya Venkat aarya@uga.edu; Mention mention@noreply.github.com Subject: Re: [Electrostatics/apbs-pdb2pqr] NotImplementedError: PDB2PKA not implemented. (#615)

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

@arikathttps://github.com/arikat If you are still seeing that error, can you provide is with OS, python version, which distribution (e.g. apbs-pdb2pqr-vPDB2PQR-2.1.1-release.tar.gz, apbs-pdb2pqr-vPDB2PQR-2.1.1-release.zip, etc.), how are you invoking pdb2pqr from the command line, and if possible the pdf file as well? Thanks!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/Electrostatics/apbs-pdb2pqr/issues/615#issuecomment-649601352, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AKIZAOY27G5Z2OVKUF4M6ILRYNQQ3ANCNFSM4OHQMFAA.

sobolevnrm commented 4 years ago

@kozlac - could you please look into this?

kozlac commented 4 years ago

Hello @arikat, a couple of things:

I downloaded this version and the 1t8l.pdb from the PDB website and ran the following command successfully:

pdb2pqr --ff parse --ph-calc-method pdb2pka --pdb2pka-out ./temp 1t8l.pdb output.pqr

Notice you don't need to put python at the beginning of the command. Please let me know if you have any problems. Thanks!

arikat commented 4 years ago

Sorry, the python3 was a typo. I'll try this command thanks!

Aarya Venkat

Biochemistry PhD Student, Kannan Lab

Future Faculty Fellow

University of Georgia

https://arikat.github.io/

From: Juan notifications@github.com Sent: Thursday, June 25, 2020 1:49 PM To: Electrostatics/apbs-pdb2pqr apbs-pdb2pqr@noreply.github.com Cc: Aarya Venkat aarya@uga.edu; Mention mention@noreply.github.com Subject: Re: [Electrostatics/apbs-pdb2pqr] NotImplementedError: PDB2PKA not implemented. (#615)

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

Hello @arikathttps://github.com/arikat, a couple of things:

I downloaded this versionhttps://github.com/Electrostatics/apbs-pdb2pqr/releases/download/vPDB2PQR-2.1.1/pdb2pqr-linux-bin64-2.1.1.tar.gz and the 1t8l.pdb from the PDB website and ran the following command successfully:

pdb2pqr --ff parse --ph-calc-method pdb2pka --pdb2pka-out ./temp 1t8l.pdb output.pqr

Notice you don't need to put python at the beginning of the command. Please let me know if you have any problems. Thanks!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/Electrostatics/apbs-pdb2pqr/issues/615#issuecomment-649727985, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AKIZAO7VJYFPK33O5F446E3RYOEZ5ANCNFSM4OHQMFAA.

arikat commented 4 years ago

This command worked, thank you!

Aarya Venkat

Biochemistry PhD Student, Kannan Lab

Future Faculty Fellow

University of Georgia

https://arikat.github.io/

From: Juan notifications@github.com Sent: Thursday, June 25, 2020 1:49 PM To: Electrostatics/apbs-pdb2pqr apbs-pdb2pqr@noreply.github.com Cc: Aarya Venkat aarya@uga.edu; Mention mention@noreply.github.com Subject: Re: [Electrostatics/apbs-pdb2pqr] NotImplementedError: PDB2PKA not implemented. (#615)

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

Hello @arikathttps://github.com/arikat, a couple of things:

I downloaded this versionhttps://github.com/Electrostatics/apbs-pdb2pqr/releases/download/vPDB2PQR-2.1.1/pdb2pqr-linux-bin64-2.1.1.tar.gz and the 1t8l.pdb from the PDB website and ran the following command successfully:

pdb2pqr --ff parse --ph-calc-method pdb2pka --pdb2pka-out ./temp 1t8l.pdb output.pqr

Notice you don't need to put python at the beginning of the command. Please let me know if you have any problems. Thanks!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/Electrostatics/apbs-pdb2pqr/issues/615#issuecomment-649727985, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AKIZAO7VJYFPK33O5F446E3RYOEZ5ANCNFSM4OHQMFAA.

kozlac commented 4 years ago

Great!