#34 large tasks and list filtering

[Jacek Plewka]

Dear All,

I am writing here with two requests:

• I run 170 000 dockings and after 5 days of work the software died by itself. Is it possible to retrieve this data (not saved) and make program more stable (0.9.8 on Win10).
• could you please add a feature to filter imported ligands by e.g. number of atoms so that they appear on the top of the list and then allow to delete a selection from the list? Ofthen when importing a list of ligands that was not defined by me I have e.g. ions, sugars, atoms, buffers that I am not interested in and I have to delete them manually every time.

Best regards,

Jacek

[Sarkis Dallakian]

Dear Jacek,

You can look in your home folder under .PyRx_workspace\Macromolecules\your protein name for out.pdbqt files that are Vina output files. I think it might have run out of memory that's why it died. You can load them using + icon on Analyze Results tab. You might need to add more RAM to fit all docking in memory. How much is your current RAM and how many docking results you can fit there?

You can use Open Babel widget to filter ligands by number of atoms, logP, weight or Lipinski rule of five. I've added a new feature in Open Babel widget so that you can open multiple molecules at once. Please use PyRx > Help > Check for Updates... menu to apply this update.

Best regards,
Sarkis

[Jacek Plewka]

?Dear Sarkis,

thank you for your interest. I indeed found the folder with data saved. I currently have 32gb ram, which seems to work well until 5-5.5k compounds. After that PyRX simply crashes. For now i manually remove docked ligands from the folder and do docking in 3k packages.

I do have though a follow-up question. Docking does sth weird to my compounds. I can nicely recreate binding position from the crystal, but the hydrogens within cyclohexane ring collapse together creating this mess in pymol and also in 2D structure (connected carbons). Do you know how to fix it? On top of that, is PyRX sensitive enough to dock stereocenters in R/S positions? In theory, the bottom drawing shows it, but I get plenty of compounds where all or some centers are not defined.

[cid:b9a3b1d6-e3c3-4d78-ba37-2b17768af77d]?

I am looking forward to hearing from you.

Best regards from in-silico docking enthusiast,

Jacek

Jacek Plewka, PhD

---

Faculty of Chemistry, Jagiellonian University
Gronostajowa 2, 30-387 Krakow, Poland
e-mail: jacek.plewka@uj.edu.pl
work: 0048-12-686-2435

---

Od: Sarkis Dallakian sarkiss@users.sourceforge.net
Wysłane: 7 maja 2019 04:04
Do: [pyrx:tickets]
Temat: [pyrx:tickets] #34 large tasks and list filtering

Dear Jacek,

You can look in your home folder under .PyRx_workspace\Macromolecules\you protein name for out.pdbqt files that are Vina output files. I think it might have run out of memory that's why it died. You can load them using + icon on Analyze Results tab. You might need to add more RAM to fit all docking in memory. How much is your current RAM and how many docking results you can fit there?

You can use Open Babel widget to filter ligands by number of atoms, logP, weight or Lipinski rule of five. I've added a new feature in Open Babel widget so that you can open multiple molecules at once. Please use PyRx > Help > Check for Updates... menu to apply this update.

Best regards,
Sarkis

---

[tickets:#34]https://sourceforge.net/p/pyrx/tickets/34/ large tasks and list filtering

Status: open
Milestone: 0.9.x
Created: Mon May 06, 2019 07:31 AM UTC by Jacek Plewka
Last Updated: Mon May 06, 2019 07:31 AM UTC
Owner: nobody

Dear All,

I am writing here with two requests:

• I run 170 000 dockings and after 5 days of work the software died by itself. Is it possible to retrieve this data (not saved) and make program more stable (0.9.8 on Win10).
• could you please add a feature to filter imported ligands by e.g. number of atoms so that they appear on the top of the list and then allow to delete a selection from the list? Ofthen when importing a list of ligands that was not defined by me I have e.g. ions, sugars, atoms, buffers that I am not interested in and I have to delete them manually every time.

Best regards,

Jacek

---

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[Sarkis Dallakian]

Dear Jacek,

Glad you found the folder with data saved. Doing docking in 3k packages sounds good.

For 2D structure (connected carbons), you can use Open Babel widget to minimize the ligand. This happens because atoms are too close to each other. After energy minimization it should display them fine.

Best regards,
Sarkis

[Jacek Plewka]

Dear Sarkis,

Up to minimalization and transformation to pdbqt with open babel aplet everything is fine. It is the torsions of docking that causes those issues.

Nevertheless, thank you for your assistance.

Best regards,

Jacek

Jacek Plewka, PhD

---

Faculty of Chemistry, Jagiellonian University
Gronostajowa 2, 30-387 Krakow, Poland
e-mail: jacek.plewka@uj.edu.pl
work: 0048-12-686-2435

From: Sarkis Dallakiansarkiss@users.sourceforge.net
Sent: Friday, May 10, 2019 2:27 AM
To: [pyrx:tickets] 34@tickets.pyrx.p.re.sourceforge.net
Subject: [pyrx:tickets] Re: #34 large tasks and list filtering

Dear Jacek,

Glad you found the folder with data saved. Doing docking in 3k packages sounds good.

For 2D structure (connected carbons), you can use Open Babel widget to minimize the ligand. This happens because atoms are too close to each other. After energy minimization it should display them fine.

Best regards,
Sarkis

---

[tickets:#34]https://sourceforge.net/p/pyrx/tickets/34/ large tasks and list filtering

Status: open
Milestone: 0.9.x
Created: Mon May 06, 2019 07:31 AM UTC by Jacek Plewka
Last Updated: Tue May 07, 2019 02:04 AM UTC
Owner: nobody

Dear All,

I am writing here with two requests:

• I run 170 000 dockings and after 5 days of work the software died by itself. Is it possible to retrieve this data (not saved) and make program more stable (0.9.8 on Win10).
• could you please add a feature to filter imported ligands by e.g. number of atoms so that they appear on the top of the list and then allow to delete a selection from the list? Ofthen when importing a list of ligands that was not defined by me I have e.g. ions, sugars, atoms, buffers that I am not interested in and I have to delete them manually every time.

Best regards,

Jacek

---

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