Macromolecule pdbqt file formation error

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Macromolecule pdbqt file formation error

Postby mai el-naggar » Thu Jun 11, 2015 5:27 pm

Can PyRx 0.8 work properly if I am using Windows 8.1 as operating system?
It is the first time (after using it with windows 8.1) to ask me to select conformation for each amino acid residue (A or B) when I make macromolecule, then it produced the following error
Wxpython: stdout/stderr
Traceback (most recent call last):
File "C:\Program Files (x86)\PyRx\lib\site-packages\PyRx\molNavigator.py", line 136, in OnMakeMacromolecule
mol = self.frame.autodockNav.AddMacromolecule(mol)
File "C:\Program Files (x86)\PyRx\lib\site-packages\PyRx\autodockNavigator.py", line 66, in AddMacromolecule
mol = self.SelectAlternate(mol)
File "C:\Program Files (x86)\PyRx\lib\site-packages\PyRx\autodockNavigator.py", line 143, in SelectAlternate
self.vsModel.PrepareReceptorMol(mol)
File "C:\Program Files (x86)\PyRx\lib\site-packages\PyRx\vsModel.py", line 358, in PrepareReceptorMol
RPO = AD4ReceptorPreparation(mol, outputfilename=outputfilename)
File "C:\Program Files (x86)\PyRx\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 546, in __init__
version=version, delete_single_nonstd_residues=delete_single_nonstd_residues)
File "C:\Program Files (x86)\PyRx\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 123, in __init__
self.repairMol(mol, self.repair_type_list)
File "C:\Program Files (x86)\PyRx\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 178, in repairMol
self.newHs = self.addHydrogens(mol)
File "C:\Program Files (x86)\PyRx\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 186, in addHydrogens
HB.addHydrogens(mol)
File "C:\Program Files (x86)\PyRx\lib\site-packages\MolKit\hydrogenBuilder.py", line 100, in addHydrogens
childIndex = res.children.index(heavyAtom)+1
File "C:\Program Files (x86)\PyRx\lib\UserList.py", line 81, in index
def index(self, item, *args): return self.data.index(item, *args)
ValueError: list.index(x): x not in list
What shall I do?
Thank you
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mai el-naggar
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Re: Macromolecule pdbqt file formation error

Postby sargis » Thu Jun 11, 2015 11:07 pm

Thank you for the message. Would you please upload the pdb of the macromolecule? I've fixed many bugs related to making pdbqt with alternate conformation since PyRx 0.8. Not sure, if this bug is already fixed in the latest version.
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Re: Macromolecule pdbqt file formation error

Postby mai el-naggar » Sun Jun 14, 2015 6:09 am

Dear Sargis,
Thank you so much for your reply. I am sorry I can't upload the pdb of the macromolecule here because the file is too big. The pdb code for this macromolecule is 2dux.
Thank you so much
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Re: Macromolecule pdbqt file formation error

Postby sargis » Sun Jun 14, 2015 5:06 pm

Yo
mai el-naggar wrote:Thank you so much for your reply. I am sorry I can't upload the pdb of the macromolecule here because the file is too big. The pdb code for this macromolecule is 2dux.
Thank you so much

You are very welcome and thank you for the pdb code. I've used latest version of PyRx (0.9) and it worked fine. I'm uploading converted pdbqt here:
2dux.pdbqt
(242.63 KiB) Downloaded 212 times
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Re: Macromolecule pdbqt file formation error

Postby mai el-naggar » Sun Jun 14, 2015 10:59 pm

Thank you so much Sargis.
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