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pdbqt ligand file
http://mgl.scripps.edu/forum/viewtopic.php?f=11&t=3236
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Author:  Hanane [ Thu May 05, 2016 12:12 pm ]
Post subject:  pdbqt ligand file

Hi Everybody I started recentely working with autodock vina on windows and I find Some difficulties withe my ligand pdpqt file can anyone help me, I convert my ligand file from sdf to pdpqt file using openbabel, but whene i ty to open it ,warning message appears, contains (5 molecules in the file ), and python shel window appears contains
****************************************************************
Personal firewall software may warn about the connection IDLE
makes to its subprocess using this computer's internal loopback
interface. This connection is not visible on any external
interface and no data is sent to or received from the Internet.
****************************************************************

IDLE 1.2.2 ==== No Subprocess ====
>>> Error parsing the following line in pdb:
ATOM 1 C LIG 1 5,000 28,000 5,000 0.00 0.00 +0,183 C

ERROR *********************************************
Traceback (most recent call last):
File "C:\Program Files\MGLTools-1.5.6\lib\site-packages\ViewerFramework\VF.py", line 898, in tryto
result = command( *args, **kw )
File "C:\Program Files\MGLTools-1.5.6\lib\site-packages\Pmv\fileCommands.py", line 1176, in doit
mols = newparser.parse()
File "C:\Program Files\MGLTools-1.5.6\lib\site-packages\MolKit\pdbParser.py", line 657, in parse
self.pdbRecordParser[record](self.allLines, self.mol)
File "C:\Program Files\MGLTools-1.5.6\lib\site-packages\MolKit\pdbParser.py", line 431, in parse_PDB_atoms
at = self.parse_PDB_ATOM_record(atRec, mol)
File "C:\Program Files\MGLTools-1.5.6\lib\site-packages\MolKit\pdbParser.py", line 2318, in parse_PDB_ATOM_record
atom._coords = [ [ float(rec[30:38]), float(rec[38:46]),
ValueError: invalid literal for float(): 5,000
ERROR *********************************************
Traceback (most recent call last):
File "C:\Program Files\MGLTools-1.5.6\lib\site-packages\ViewerFramework\VF.py", line 898, in tryto
result = command( *args, **kw )
File "C:\Program Files\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autotorsCommands.py", line 996, in doit
numAts = len(m.allAtoms)
AttributeError: 'str' object has no attribute 'allAtoms'

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