I am using obabel tool to batch convert a set of SDF
files to PDB
file.
obabel *.sdf -opdb --gen3d -m
I have ~50000 files and i am getting totally of 12 warnings in total (warning mentioned below).
==============================
*** Open Babel Warning in CorrectStereoAtoms
Could not correct 2 stereocenter(s) in this molecule ()
with Atom Ids as follows: 1 5
Warning: Stereochemistry is wrong, using the distance geometry method instead
==============================
*** Open Babel Warning in CorrectStereoAtoms
Could not correct 2 stereocenter(s) in this molecule ()
with Atom Ids as follows: 2 4
Warning: Stereochemistry is wrong, using the distance geometry method instead
==============================
*** Open Babel Warning in CorrectStereoAtoms
Could not correct 3 stereocenter(s) in this molecule ()
with Atom Ids as follows: 1 3 4
Warning: Stereochemistry is wrong, using the distance geometry method instead
==============================
*** Open Babel Warning in CorrectStereoAtoms
Could not correct 4 stereocenter(s) in this molecule ()
with Atom Ids as follows: 0 2 3 4
Warning: Stereochemistry is wrong, using the distance geometry method instead
==============================
*** Open Babel Warning in CorrectStereoAtoms
Could not correct 2 stereocenter(s) in this molecule ()
with Atom Ids as follows: 1 12
Warning: Stereochemistry is wrong, using the distance geometry method instead
==============================
*** Open Babel Warning in CorrectStereoAtoms
Could not correct 1 stereocenter(s) in this molecule ()
with Atom Ids as follows: 0
Warning: Stereochemistry is wrong, using the distance geometry method instead
==============================
*** Open Babel Warning in CorrectStereoAtoms
Could not correct 1 stereocenter(s) in this molecule ()
with Atom Ids as follows: 1
Warning: Stereochemistry is wrong, using the distance geometry method instead
==============================
*** Open Babel Warning in CorrectStereoAtoms
Could not correct 2 stereocenter(s) in this molecule ()
with Atom Ids as follows: 0 2
Warning: Stereochemistry is wrong, using the distance geometry method instead
==============================
*** Open Babel Warning in CorrectStereoAtoms
Could not correct 2 stereocenter(s) in this molecule ()
with Atom Ids as follows: 0 11
Warning: Stereochemistry is wrong, using the distance geometry method instead
==============================
*** Open Babel Warning in CorrectStereoAtoms
Could not correct 3 stereocenter(s) in this molecule ()
with Atom Ids as follows: 0 2 13
Warning: Stereochemistry is wrong, using the distance geometry method instead
==============================
*** Open Babel Warning in CorrectStereoAtoms
Could not correct 1 stereocenter(s) in this molecule ()
with Atom Ids as follows: 0
Warning: Stereochemistry is wrong, using the distance geometry method instead
==============================
*** Open Babel Warning in CorrectStereoAtoms
Could not correct 1 stereocenter(s) in this molecule ()
with Atom Ids as follows: 0
Warning: Stereochemistry is wrong, using the distance geometry method instead
==============================
*** Open Babel Warning in CorrectStereoAtoms
Could not correct 1 stereocenter(s) in this molecule ()
with Atom Ids as follows: 0
Warning: Stereochemistry is wrong, using the distance geometry method instead
==============================
*** Open Babel Warning in CorrectStereoAtoms
Could not correct 1 stereocenter(s) in this molecule ()
with Atom Ids as follows: 0
Warning: Stereochemistry is wrong, using the distance geometry method instead
==============================
*** Open Babel Warning in CorrectStereoAtoms
Could not correct 5 stereocenter(s) in this molecule ()
with Atom Ids as follows: 8 9 30 31 52
Warning: Stereochemistry is wrong, using the distance geometry method instead
How do I identify the exact 12 files which have created this warning?
Edit:
As suggested, I tried to use --errorlevel 3. But sadly, that also did not help to identify the exact ligand throwing out the error. I am pasting the output got with the code. It is similar to the earlier one.
obabel *.sdf -opdb --gen3d --errorlevel 3 -m
obabel *.sdf -opdb --gen3d --errorlevel 3 -m
==============================
*** Open Babel Warning in CorrectStereoAtoms
Could not correct 2 stereocenter(s) in this molecule ()
with Atom Ids as follows: 1 5
Warning: Stereochemistry is wrong, using the distance geometry method instead
==============================
*** Open Babel Warning in CorrectStereoAtoms
Could not correct 2 stereocenter(s) in this molecule ()
with Atom Ids as follows: 2 4
Warning: Stereochemistry is wrong, using the distance geometry method instead
==============================
*** Open Babel Warning in CorrectStereoAtoms
Could not correct 3 stereocenter(s) in this molecule ()
with Atom Ids as follows: 1 3 4
Warning: Stereochemistry is wrong, using the distance geometry method instead
==============================
*** Open Babel Warning in CorrectStereoAtoms
Could not correct 4 stereocenter(s) in this molecule ()
with Atom Ids as follows: 0 2 3 4
Warning: Stereochemistry is wrong, using the distance geometry method instead
==============================
*** Open Babel Warning in CorrectStereoAtoms
Could not correct 2 stereocenter(s) in this molecule ()
with Atom Ids as follows: 1 12
Warning: Stereochemistry is wrong, using the distance geometry method instead
for i in *.sdf; do echo "$i"; obabel "$i" -opdb --gen3d -m; done
instead---errorlevel 3
or similar (the online manual says "---errorlevel <N> Filter the level of errors and warnings displayed: 1 = critical errors only 2 = include warnings too (default) 3 = include informational messages too"error level 3
with the following codeobabel *.sdf -opdb --gen3d --errorlevel 3 -m
. Going on. I think it is going to be bit slow. Will update on completion