ADL: adcovalent error

Pedro Miguel Reis Figueiredo pmrfigueiredo at cnc.uc.pt
Wed Nov 25 04:32:45 PST 2020


Hi, 

I am trying to do a covalent docking following the tutorial present
here: Covalent docking -- AutoDock (scripps.edu) [1]. I having trouble
following the tutorial with the provided files for 3upo with the
following error message: 

$ PYTHON2.7 SCRIPTS/PREPARECOVALENT.PY --LIGAND LIGAND.MOL2 --LIGINDICES
4,3 --LIGSMART "C(=O)-O-C" --RECEPTOR 3UPO_PROTEIN.PDB --RESIDUE
B:SER222 --OUTPUTFILE LIGCOVALENT.PDB 

Processing residue B:SER222
[start] output filename is: ligcovalent.pdb
Traceback (most recent call last):
File "scripts/prepareCovalent.py", line 1318, in <module>
x = CovalentDockingMaster()
File "scripts/prepareCovalent.py", line 870, in __init__
self.start()
File "scripts/prepareCovalent.py", line 1261, in start
self.processResidues()
File "scripts/prepareCovalent.py", line 1297, in processResidues
aligner = self.x = CovalentDockingMaker(**self.alignerArgs)
File "scripts/prepareCovalent.py", line 231, in __init__
self.process()
File "scripts/prepareCovalent.py", line 277, in process
self.align()
File "scripts/prepareCovalent.py", line 341, in align
verbose=self.verbose, debug=self.debug)
File "scripts/prepareCovalent.py", line 681, in __init__
self.align()
File "scripts/prepareCovalent.py", line 687, in align
self.translate()
File "scripts/prepareCovalent.py", line 754, in translate
translation = vector( self._ligA, self._recI)
File "scripts/prepareCovalent.py", line 76, in vector
if not p2 == None:
ValueError: The truth value of an array with more than one element is
ambiguous. Use a.any() or a.all() 

The same happens when I try to submit this job without the SMART
parameter: 

$ PYTHON2.7 SCRIPTS/PREPARECOVALENT.PY --LIGAND LIGAND.MOL2 --LIGINDICES
1,2 --RECEPTOR 3UPO_PROTEIN.PDB --RESIDUE B:SER222 --OUTPUTFILE
LIGCOVALENT.PDB 

Any ideas on how can I get over this error? 

Thank you in advance! 

Links:
------
[1] http://autodock.scripps.edu/resources/covalentdocking






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