Dear lab team,
I'm a student in Tel-Aviv university working on the problem of predicting DDG and I'm trying to use your standalone DDG predictor in order to reproduce the reported results of your method.
I downloaded your BindProfX suite, and I followed the attached readme which instructed me to follow another readme which instructed me to download some files from the following link:
http://foldxsuite.crg.eu/node/732/download/448ff7cb87c60cefe85dfc66145e87e2
I proceeded to installing Biopython (you didn't specify which version so I installed the newest 1.72).
I ran your get_final_score.py script on the input in your demo dir (kindly see attached):
python2 get_final_score.py XBindProf/demo/
and I am getting the following error from Biopython:
Traceback (most recent call last):
File "get_final_score.py", line 357, in
get_final_score(os.path.abspath(arg))
File "get_final_score.py", line 248, in get_final_score
resi_dict,inv_resi_dict=reindex_complex(mutlist_file,pdb_file,mutlist_tmp,pdb_tmp)
File "/home/yotamfr/Downloads/BindProfX.2017-03-04/bin/module/reindex_complex.py", line 43, in reindex_complex
residue.id=(residue.id[0],index,residue.id[-1])
File "/home/yotamfr/.local/lib/python2.7/site-packages/Bio/PDB/Entity.py", line 173, in id
" this entity.".format(self._id, value, value))
ValueError: Cannot change id from `(' ', 1, ' ')` to `(' ', 1, ' ')`. The id `(' ', 1, ' ')` is already used for a sibling of this entity.
I tried different inputs but I always get the same error. Kindly provide me with your exact configuration, and the Biopython version you're using so I can reproduce your results.
Best regards,
Yotam