Error in PyRx

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Error in PyRx

Postby Aloysius » Fri Oct 17, 2014 6:01 am

Hello Sargis, I had installed PyRx version 0.8 in window 8, 64-bit operating system, x64-based processor and with python 2.7.8 ,microsoft visual C++ 2012.But when I used openbabel to convert the file from sdf to pbdqt and for energy minimization there have Runtime Error, Program:C:\Program Files (x86)\Pyrx\pythonw.exe.This application has requested the Runtime to terminate it in an unusual way and pythonw.exe has stopped working.The tittle of the error is Microsoft Visual C++ Runtime library.

Thank You

Regards
Aloysius
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Re: Error in PyRx

Postby sargis » Sun Oct 19, 2014 1:23 am

Hello Aloysius,

Thank you for the message and sorry about that. There is probably caused by some strange sdf file. If you can upload that sdf as an attachment, it might be possible to see what's causing this error.

Thank you for using PyRx!
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Re: Error in PyRx

Postby Aloysius » Mon Oct 20, 2014 4:20 pm

Hi, Sargis,

Thank you for reply, The (1_p0.0) file was downloaded from Zinc database , standard lead-like.The (1_p0.0) file contain multiple of compounds, there will be an error and take very long time to load this file into pyrx. However (A) file was abstracted from (1_p0.0)file, this file (A) only contain one compound, there will not have an error to load this file into pyrx. Unfortunately I can't upload the (1_p0.0) file because is too big.

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Aloysius
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Re: Error in PyRx

Postby sargis » Mon Oct 20, 2014 11:30 pm

Hi Aloysius,

Thank you for the sdf file. I've looked at the standard lead-like molecules page from the Zinc database and there are more than 6 million molecules there. I haven't tried loading this type of large sdf into pyrx. Sorry that it takes very long time to load this file into pyrx. You'll need to find which molecule causes error to troubleshoot this. You can find it by comparing which molecules pyrx converted to pdbqt and where it failed by going down the list in the Open Babel table.

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Sargis
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Re: Error in PyRx

Postby Aloysius » Sat Nov 01, 2014 12:08 pm

Hi Sargis,

Due to the problem with sdf file format, I have decided to change sdf to mol2 file. And mol2 loaded faster into pyrx compare to sdf file.But I still get an error during energy minimization. The error is unhandled exception (An unhandled exception occurned. Press abort to terminate the program. Retry to exist the program normally. Ignore to try to continue.)How can I solve this ? Whether I press retry or ignore the program will stop working.

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Re: Error in PyRx

Postby sargis » Sat Nov 01, 2014 8:52 pm

Hi Aloysius,

Thank you for the update. Glad to know that mol2 loaded faster into pyrx compare to sdf file. To handle the error during energy minimization, you can try minimizing that molecule using a different force field. Under PyRx -> Preferences... -> Open Babel there are two other force fields (mmff94 and ghemical) you can try.

Also see if you can find 3d structure of that molecule in PubChem or elsewhere. One of the pyrx users recently asked me for help making pdbqt of cisplatin. There was no 3d structure of cisplatin PubChem and http://www.drugbank.ca/drugs/DB00515 is the only place I could find correct 3d structure of cisplatin.

You can also isolate that molecule causing error, try energy minimization with the latest version of Open Babel and submit a bug report at http://sourceforge.net/p/openbabel/bugs/ if the problem is still there.

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Re: Error in PyRx

Postby Aloysius » Tue Dec 02, 2014 11:40 am

Hi Sargis,

Good day, Recently I have completed running virtual screening on Pyrx. But I have a trouble on extracting the results, first when I click on the icon on the toolbar to open the Data plotting dialog but it pop out an error, the error messages are showed below.Second , How can I store the binding structure of my ligand and macromolecules (after run vina) in a pdf file or other file format.

Thank you

Best Regards
Aloysius
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Re: Error in PyRx

Postby sargis » Wed Dec 03, 2014 2:35 am

Hi Aloysius,

Good day to you too. The error with the Data plotting dialog has been fixed in PyRx 0.9. For the second question, you can save docked ligands as sdf file. See last image in http://pyrx.sourceforge.net/blog/97-pyr ... nouncement

I'm working on having an option to save docked macromolecule and ligand complex as PDB file. This will be available in upcoming release of PyRx 0.9.3.

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Re: Error in PyRx

Postby Aloysius » Wed Dec 03, 2014 5:33 am

Hi Sargis

Thank you for the reply. I'm running PyRx version 0.8 on Window, because only PyRx version 0.8 available download for free. Is version 0.9 available download for free too ? In the downloads menu only version 0.8 for free and 0.92 for purchase. I'm just degree student and I use PyRx for my final year project. It is sad to said I have not funding for my project,therefore I only can use open source software.

Thank you again

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Re: Error in PyRx

Postby sargis » Thu Dec 04, 2014 4:43 am

Hi Aloysius,

You are welcome. PyRx is currently available for a very low price. It will pay for itself in no time once you start running remote jobs, considering what the CPU usage prices are. No one, including myself, is willing to work on PyRx for free. There are also additional costs involved in running open source software, besides labor of love. See also "free beer" vs "free speech" distinction - http://en.wikipedia.org/wiki/Gratis_versus_libre

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