search

jensengroup / propka

PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.
http://propka.org
GNU Lesser General Public License v2.1
258 stars 58 forks source link

Error: "IndexError: list index out of range" with a specific pdb file #97

Closed toontun closed 3 years ago

toontun commented 3 years ago

Hello (again),

I got an error when I try to run propka on this pdb file: https://ufile.io/x7078g3y.

I try on other version of propka and it seems to work.

What's wrong?

Thank in advance, Best regards, toontun

sobolevnrm commented 3 years ago

Hello. I am suspicious of that link. Can you please attach the file to this issue (may need to add .txt to filename per https://docs.github.com/en/free-pro-team@latest/github/managing-your-work-on-github/file-attachments-on-issues-and-pull-requests

Also, can you please say which version of PROPKA is giving you problems and which one worked in the past?

Thank you

toontun commented 3 years ago

Hello, Yes I understand. I attached the file to this issue.

The version which gave me problems is the current version. I cloned this repo and proceeded to a pip install . .

After verification , the other version gave me problems too.

Here the pdb file: antibody1.txt

Thank you

sobolevnrm commented 3 years ago

The problem appears to be with 7314- CG 946-ASN (D) [ 109.540 188.020 98.250] C (ASN 946 on chain D). Is there anything special about this residue?

On Mon, Nov 16, 2020 at 1:17 AM toontun notifications@github.com wrote:

Hello, Yes I understand. I attached the file to this issue.

The version which gave me problems is the current version. I cloned this repo and proceeded to a pip install . .

After verification , the other version gave me problems too.

Here the pdb file: antibody1.txt https://github.com/jensengroup/propka/files/5545245/antibody1.txt

Thank you

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/jensengroup/propka/issues/97#issuecomment-727847847, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAOX7WA5GIQJZNTXY6UCAVTSQDU3LANCNFSM4TTMFCGA .

toontun commented 3 years ago

No, this residue has nothing particular.

The problem appears to be with 7314- CG 946-ASN (D) [ 109.540 188.020 98.250] C (ASN 946 on chain D). Is there anything special about this residue? … On Mon, Nov 16, 2020 at 1:17 AM toontun @.***> wrote: Hello, Yes I understand. I attached the file to this issue. The version which gave me problems is the current version. I cloned this repo and proceeded to a pip install . . After verification , the other version gave me problems too. Here the pdb file: antibody1.txt https://github.com/jensengroup/propka/files/5545245/antibody1.txt Thank you — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#97 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAOX7WA5GIQJZNTXY6UCAVTSQDU3LANCNFSM4TTMFCGA .

speleo3 commented 3 years ago

@sobolevnrm I see you self-assigned this, do you already have a solution? Because I think I found the problem (and a solution), the function BondMaker.put_atom_in_box doesn't cover all necessary neighbor cells.

sobolevnrm commented 3 years ago

@sobolevnrm I see you self-assigned this, do you already have a solution? Because I think I found the problem (and a solution), the function BondMaker.put_atom_in_box doesn't cover all necessary neighbor cells.

I do not have a solution -- thanks for troubleshooting this!

toontun commented 3 years ago

Thank you!