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some problem on prepare_covalent_flexres.py
http://mgl.scripps.edu/forum/viewtopic.php?f=11&t=3218
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Author:  leisure [ Wed Apr 20, 2016 10:51 am ]
Post subject:  some problem on prepare_covalent_flexres.py

recently, i want to have a covalent docking by means of autodock4.2. i want to use flexible side-chain method to do it. what i do firstly is the move ligand to the target atom of receptor. what the atom of my exercise is CYS164. i found prepare_covalent_flexres.py can help me to do this.
but i met some problems in using this script.
the first one is i imitate the example of the 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

the following is my job :
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
setting PYTHONHOME environment
Traceback (most recent call last):
File "prepare_covalent_flexres.py", line 282, in <module>
assert len(at_names)==3
AssertionError
from it feedback we can know it must have three atom.

please give me some guidence.

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