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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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Broken biomolecule with pdb2pqr30 but works on webserver. #192

Closed marcushock closed 2 years ago

marcushock commented 3 years ago

I'm trying to convert a PDB structure of myosin from an MD simulation into a pqr file. When using the web server online, I am able to successfully convert it, however using the command line interface, I'm having issues, and get the error that there is a gap in the biomolecule structure. In the command line interface I'm using the command: pdb2pqr30 --titration-state-method=propka --with-ph=7 --ff=PARSE --whitespace --drop-water myosin.pdb myosin.pqr

I'm using the same settings on the webserver where it works. Also, this is using pdb2pqr30 version 3.4.0.

I've attached the myosin structure that I'm having issues with.

myosin.zip

mishaguy commented 2 years ago

have you resolved this issue?

marcushock commented 2 years ago

I have not yet solved this issue. It looks like the web version no longer works either for my system. I have found that a previous version that is part of PyMol still works though. Unfortunately I don't know the exact version coupled with PyMol. pdb2pqr --version just returns pdb2pqr (Version @PDB2PQR_VERSION@)

mishaguy commented 2 years ago

thanks for your reply. we found issues now with current default pdb2pqr when running from PyMol. It is failing on many RNA molecules fetched from pdb. It is on Windows. It is version 3.2.0. The error points to biomolecule.py indicating that it can't find RA in the structure. It is strange because it it there. The same molecules processed nicely on web service although they have different options. I tried with their options and still got error. Are you on Windows or on Linux (on Mac it is different distribution of PyMol). I thought we might have similar issue. thanks

sobolevnrm commented 2 years ago

We have upgraded the webserver. Do you have a structure we can use to test if the problem persists after the upgrade?

mishaguy commented 2 years ago

Hi Nathan,

Thanks for thinking about me.

First of all, it is not on the webserver where this error occurs. It is rather when I use pdb2pqr from PyMol plugin.

I have updated now to your 3.2.2 and no, it is still producing error with default pd2pqr method.

It is now actually producing more complicated error log than 3.2.0. I have attached it here.

The structure producing error is for instance 4e8m.

Hope this will be resolved soon and thanks for the great tool you provide to research community.

Best, Misha pdb2pqr.log

sobolevnrm commented 2 years ago

Hi Misha --

I don't know much about PyMOL but am wondering if @speleo3 could suggest someone to help.

What version of Python does your PyMOL use?

Thanks

sobolevnrm commented 2 years ago

This PyMOL issue appears to be a duplicate of #236

marcushock commented 2 years ago

Sorry about the delay responding, I am still having issues however. I've attached the molecule I'm having issues with in the original post. (myozin.zip) Interestingly, previous versions (such as from PyMol) do not have any issues.

speleo3 commented 2 years ago

I can reproduce this without PyMOL, using the latest PDB2PQR (v3.4.0, cc31e1351bcd).

pdb2pqr30 --ff=AMBER myosin.pdb out.pqr

CRITICAL:Unable to debump biomolecule. Biomolecular structure is incomplete: Found gap in biomolecule structure for atom ATOM 12959 H2 PRO 813 211.335 243.791 177.912 0.0000 0.0000 CRITICAL:Giving up.

Residues 810-812 are missing. PRO 813 has two hydrogens (H2 and H3).

No such error with PDB2PQR 2.1.2

Edit: Corrected statement about capping atom

speleo3 commented 2 years ago

There is a DA residue with residue number 812 (right before PRO 813), but it's not an amino acid and it's not connected to PRO 813. Changing its chain identifier from A to B fixes the issue for me.

sobolevnrm commented 2 years ago

Thank you!

mishaguy commented 2 years ago

Hi, thanks for this.

One note, I did understand from the beginning that I could fix this issue in structure myself. However, I can’t advise my users to do this. They are just scientists and not away what is going on in background.

It might be PDB issue. However, as you mentioned it does not occur with previous pdb2pqr.

Best, Misha

Mikhael Guy Research Scientist Science Research Software Core Yale Center for Research Computing Yale University P.O. Box 208107 Sterling Chemistry Laboratory 225 Prospect Street, Rm. 154 New Haven, CT 06520 203.436.8599 For questions related to scientific, analytical and computational software, please e-mail at @.***

On Dec 18, 2021, at 10:40 AM, Nathan Baker @.***> wrote:

Thank you!

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sobolevnrm commented 2 years ago

Hi Nathan,

Thanks for thinking about me.

First of all, it is not on the webserver where this error occurs. It is rather when I use pdb2pqr from PyMol plugin.

I have updated now to your 3.2.2 and no, it is still producing error with default pd2pqr method.

It is now actually producing more complicated error log than 3.2.0. I have attached it here.

The structure producing error is for instance 4e8m.

Hope this will be resolved soon and thanks for the great tool you provide to research community.

Best, Misha pdb2pqr.log

The issue with 4E8M was just fixed in https://github.com/Electrostatics/pdb2pqr/commit/6673aabb1d424594785d5d5b36fa3cc69aec4db5.

mishaguy commented 2 years ago

Hi Nathan,

I go to web service and run 4e8m with default parameters. It still has errors. The log says it is unable to proceed and does not let to go to APBS step. I see it is running v. 3.4.0. pip actually gives me now 3.4.1 but I have the same issue. What version are you using to get all this running properly and where to get it?

Thans, Misha

Mikhael Guy Research Scientist Science Research Software Core Yale Center for Research Computing Yale University P.O. Box 208107 Sterling Chemistry Laboratory 225 Prospect Street, Rm. 154 New Haven, CT 06520 203.436.8599 For questions related to scientific, analytical and computational software, please e-mail at @.***

On Dec 30, 2021, at 10:21 PM, Nathan Baker @.***> wrote:

Hi Nathan,

Thanks for thinking about me.

First of all, it is not on the webserver where this error occurs. It is rather when I use pdb2pqr from PyMol plugin.

I have updated now to your 3.2.2 and no, it is still producing error with default pd2pqr method.

It is now actually producing more complicated error log than 3.2.0. I have attached it here.

The structure producing error is for instance 4e8m.

Hope this will be resolved soon and thanks for the great tool you provide to research community.

Best, Misha pdb2pqr.log https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FElectrostatics%2Fpdb2pqr%2Ffiles%2F7577347%2Fpdb2pqr.log&data=04%7C01%7Cmikhael.guy%40yale.edu%7Ce360fb3e7bca4661d7fd08d9cc0cafc9%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637765177137870862%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=GW64KheMjHb4TGN3VcI4IMSX1ZmQ9oPz95SwzcA3cKM%3D&reserved=0 The issue with 4E8M was just fixed in 6673aab https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FElectrostatics%2Fpdb2pqr%2Fcommit%2F6673aabb1d424594785d5d5b36fa3cc69aec4db5&data=04%7C01%7Cmikhael.guy%40yale.edu%7Ce360fb3e7bca4661d7fd08d9cc0cafc9%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637765177137870862%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=KskZ5QXdpACwHyOM68x5wfBmUCi4qWjPapQwjSRNxpg%3D&reserved=0.

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sobolevnrm commented 2 years ago

You'll have to pull it from the master branch in Git until I get a new release out (hopefully today).