Autodock problem in PyRx 0.9.4

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Autodock problem in PyRx 0.9.4

Postby Nazz » Tue May 10, 2016 3:23 pm

Hello,

I'm running PyRx 0.9.4 with 7 proteins and 40 ligands. In my test runs with 10 docks per ligand per protein, I am receiving these error messages, and while it completes the docking of 1 ligand to the 7 proteins, it is not automatically moving on to the next ligand.I have tried updating but there are no new updates at this time.

In the .dlg file it gives me the following message

DPF> map ..\XXX_a.A.map # atom-specific affinity map
D:\OldStuff\Program Files (x86)\PyRx\autodock4.exe: WARNING: Filename mismatch: "XXX_a.maps.fld" :: "..\XXX_a.maps.fld"

And in wxPython:

Traceback (most recent call last):
File "D:\OldStuff\Program Files (x86)\PyRx\lib\site-packages\wx-2.8-msw-unicode\wx\_core.py", line 14640, in <lambda>
lambda event: event.callable(*event.args, **event.kw) )
File "D:\OldStuff\Program Files (x86)\PyRx\lib\site-packages\PyRx\autodockPage.py", line 386, in CheckResults
index = self.ligands.index(ligand)
ValueError: list.index(x): x not in list

Thanks
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Re: Autodock problem in PyRx 0.9.4

Postby sargis » Wed May 11, 2016 4:02 am

Hello,

Thank you for the message and sorry about that. Would you please use File -> Export menu and send me PyRx_workspace.tar.gz it generates.

I would like to reproduce this on my end so I can help you with that.
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Re: Autodock problem in PyRx 0.9.4

Postby Nazz » Thu May 12, 2016 12:19 pm

I'm sorry but I have not been able to reduce the tar.gz file below 5GB to send to you. The issue regarding continuous running seems to have corrected itself (I'm currently running a smaller set of ligands (21) against a larger number of proteins (8)). I will get back regarding if the issue arises again when I use a full ligand set.
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Re: Autodock problem in PyRx 0.9.4

Postby sargis » Fri May 13, 2016 12:19 am

Thank you for the update. Glad to hear that this issue seems to have corrected itself. If you can find which receptor-ligand was causing this, it would be more easier to send the input files for that particular complex and I'll be happy to help with that.
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Re: Autodock problem in PyRx 0.9.4

Postby drparvinjangra » Mon Aug 01, 2016 12:16 pm

hey
ihave a problem with autodocking in pyrx 0.8 version
Traceback (most recent call last):
File "C:\Program Files\PyRx\lib\site-packages\PyRx\selectMolecules.py", line 156, in Next
self.CheckAtomTypes()
File "C:\Program Files\PyRx\lib\site-packages\PyRx\selectMolecules.py", line 174, in CheckAtomTypes
self.tree.SelectItem(self.frame.autodockNav.autodockTree.ligandTree.treeDict[path], False)
AttributeError: 'SelectMoleculesPage' object has no attribute 'tree'
how can i solve this?
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Re: Autodock problem in PyRx 0.9.4

Postby sargis » Tue Aug 02, 2016 2:25 am

drparvinjangra wrote:hey
ihave a problem with autodocking in pyrx 0.8 version
Traceback (most recent call last):
File "C:\Program Files\PyRx\lib\site-packages\PyRx\selectMolecules.py", line 156, in Next
self.CheckAtomTypes()
File "C:\Program Files\PyRx\lib\site-packages\PyRx\selectMolecules.py", line 174, in CheckAtomTypes
self.tree.SelectItem(self.frame.autodockNav.autodockTree.ligandTree.treeDict[path], False)
AttributeError: 'SelectMoleculesPage' object has no attribute 'tree'
how can i solve this?

This is probably fixed in the latest version of PyRx. You can get the latest version of PyRx for a very low price. I'll be happy to fix any bugs you might encounter with the latest version of PyRx.
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