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PostPosted: Wed Apr 20, 2016 11:00 am 
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Joined: Tue Sep 08, 2015 5:33 am
Posts: 2
recently, I want to have a covalent docking by means of autodock. according to papers, i decided to use flexible residue method to do it. so what i should do first is to add ligand to the target residue of protein. i thought prepare_covalent_flexres.py had this function. but imitating the example in the script occurs some problems。
example in script:
# To execute this command type:
# prepare_covalent_flexres.py -l filename -r receptor_filename -l ligand_to_superimpose_filename -b atom1_atom2 -R residue
#specific example:
#python -i prepare_covalent_flexres.py -r 1pwc-protein.pdbqt -l 1pwc-ligand.pdbqt -b OG_CB -R SER62 -g 1pwc_rigid.pdbqt -x 1pwc_flex.pdbqt

my job:
xres.py -r 3c9w.pdbqt -l ligand.pdbqt -b SG_CB -R CYS164 -g 3c9w_rigid.pdbqt -x 3c9w_flex.pdbqt
setting PYTHONHOME environment
Traceback (most recent call last):
File "prepare_covalent_flexres.py", line 282, in <module>
assert len(at_names)==3

according to the result, i this it must have 3 atoms, so i modified the pdbqt file, and do like this:
nobel@nobel-Precision-Tower-5810:~/autodockdone$ ./pythonsh prepare_covalent_flexres.py -r 3c9w.pdbqt -l ligand.pdbqt -b SG_CB_CA -R CYS164 -g 3c9w_rigid.pdbqt -x 3c9w_flex.pdbqt
setting PYTHONHOME environment
@@@ detected 1 clashes! @@@
C - CA = 1.5215
detected 1 clash(s)
Traceback (most recent call last):
File "prepare_covalent_flexres.py", line 438, in <module>
setAutoFlexFields(resP)
File "prepare_covalent_flexres.py", line 76, in setAutoFlexFields
rotatables = rbs.select(bondlist)
File "/home/nobel/MGLTools-1.5.6/MGLToolsPckgs/MolKit/bondSelector.py", line 535, in select
rotatable = BondOrderBondSelector().select(bnds,1)
File "/home/nobel/MGLTools-1.5.6/MGLToolsPckgs/MolKit/bondSelector.py", line 508, in select
atype.assignHybridization(allAts)
File "/home/nobel/MGLTools-1.5.6/MGLToolsPckgs/PyBabel/atomTypes.py", line 136, in assignHybridization
self.valence_three()
File "/home/nobel/MGLTools-1.5.6/MGLToolsPckgs/PyBabel/atomTypes.py", line 236, in valence_three
elif self.count_free_ox(a) >= 2: a.babel_type="Cac"
File "/home/nobel/MGLTools-1.5.6/MGLToolsPckgs/PyBabel/atomTypes.py", line 166, in count_free_ox
if bonded_atom.babel_type[0] == 'O' and \
File "/home/nobel/MGLTools-1.5.6/MGLToolsPckgs/MolKit/molecule.py", line 411, in __getattr__
raise AttributeError('member %s not found'%member)
AttributeError: member babel_type not found
nobel@nobel-Precision-Tower-5810:~/autodockdone$ ./pythonsh prepare_covalent_flexres.py -r 3c9w.pdbqt -l ligand.pdbqt -b SG_CB -R CYS164 -g 3c9w_rigid.pdbqt -x 3c9w_flex.pdbqt

please give me a help, thanks.


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