problem in making macromolecule in pdbqt format

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problem in making macromolecule in pdbqt format

Postby sam » Thu Dec 17, 2015 9:11 am

I have been trying to make a macromolecule in pdbqt format but am encountering the following error again and again
Error in : <bound method VSModel.PrepareReceptorMol of <PyRx.vsModel.VSModel instance at 0x06F704E0>>
Python 2.6.5 (r265:79096, Mar 19 2010, 21:48:26) [MSC v.1500 32 bit (Intel)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> Traceback (most recent call last):
File "C:\Program Files (x86)\PyRx\lib\site-packages\PyRx\wxMainFrame.py", line 304, in TryCommand
retObject = command(*args, **kw)
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 81, in addHydrogens
hat = AddHydrogens().addHydrogens(mol.allAtoms, method=self.method)
File "C:\Program Files (x86)\PyRx\lib\site-packages\PyBabel\addh.py", line 92, in addHydrogens
Hatoms = self.place_hydrogens1(atoms, num_H_to_add)
File "C:\Program Files (x86)\PyRx\lib\site-packages\PyBabel\addh.py", line 119, in place_hydrogens1
Hat = Hat + self.add_methyl_hydrogen(a, SP3_C_H_DIST)
File "C:\Program Files (x86)\PyRx\lib\site-packages\PyBabel\addh.py", line 303, in add_methyl_hydrogen
c3 = atom2.bonds[1].atom1.coords
File "C:\Program Files (x86)\PyRx\lib\UserList.py", line 31, in __getitem__
def __getitem__(self, i): return self.data[i]
IndexError: list index out of range
>>>
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sam
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Re: problem in making macromolecule in pdbqt format

Postby sargis » Sun Dec 20, 2015 4:20 pm

There might be something wrong with your macromolecule. I can have a loot at it if you can upload the input file here.

Thank you for using PyRx!
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Re: problem in making macromolecule in pdbqt format

Postby sam » Mon Dec 21, 2015 11:16 am

thank you for your reply.
The macromolecule is
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Re: problem in making macromolecule in pdbqt format

Postby sam » Mon Dec 21, 2015 11:19 am

The file is very large.So i have compressed it
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pdbtub.rar
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Re: problem in making macromolecule in pdbqt format

Postby sargis » Mon Dec 21, 2015 2:17 pm

Thank you for uploading this file. I see that atom CD in PRO222 (chain A) doesn't have 2 bonds that caused "list index out of range" in atom2.bonds[1].

As a workaround, you can open this with Open Babel widget, save it as *.mol2, and then open this to make a macromolecule in pdbqt format. I'm attaching pdbqt that I made using this method.
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sa.pdbqt
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