Hi, I have some problems when I use the option --gen3D. I'm trying to convert a file in SMILES format to a mol2 file in order to obtain a library suitable for virtual screening. I have 35430 fragments to convert, but for many of them I read these warnings: *** Open Babel Warning in CorrectStereoAtoms Could not correct 1 stereocenter(s) in this molecule (ZINC000242687334) with Atom Ids as follows: 5 or: *** Open Babel Warning in CorrectStereoAtoms Could not correct 1 stereocenter(s) in this molecule (ZINC000409439784) with Atom Ids as follows: 9 WARNING: damped steplength 1.67508 to 1.60548 WARNING: damped steplength 0.0118856 to 0.00859124 WARNING: damped steplength 0.0575883 to 0.00704951 or: *** Open Babel Warning in CorrectStereoAtoms Could not correct 1 stereocenter(s) in this molecule (ZINC000082411097) with Atom Ids as follows: 5 WARNING: damped steplength 0.204284 to 0.11297 WARNING: damped steplength 0.202275 to 0.11297 WARNING: damped steplength 0.176244 to 0.11297 WARNING: damped steplength 0.187 to 0.11297 WARNING: damped steplength 0.187 to 0.11297 WARNING: damped steplength 0.227796 to 0.11297 WARNING: damped steplength 0.151718 to 0.11297 WARNING: damped steplength 0.206775 to 0.11297 WARNING: damped steplength 0.471734 to 0.11297 WARNING: damped steplength 0.117905 to 0.11297 WARNING: damped steplength 0.117905 to 0.11297 WARNING: damped steplength 0.474755 to 0.11297 WARNING: damped steplength 0.124965 to 0.11297 WARNING: damped steplength 0.124965 to 0.11297 WARNING: damped steplength 0.130399 to 0.11297 WARNING: damped steplength 0.117515 to 0.11297 WARNING: damped steplength 0.118583 to 0.11297 WARNING: damped steplength 0.17073 to 0.11297 WARNING: damped steplength 0.181877 to 0.11297 WARNING: damped steplength 0.131749 to 0.11297 WARNING: damped steplength 0.141123 to 0.11297 WARNING: damped steplength 0.191387 to 0.11297 WARNING: damped steplength 0.185979 to 0.11297 WARNING: damped steplength 0.272824 to 0.11297 WARNING: damped steplength 0.272824 to 0.11297 WARNING: damped steplength 0.381204 to 0.11297 WARNING: damped steplength 0.122355 to 0.11297 WARNING: damped steplength 0.122355 to 0.11297 WARNING: damped steplength 0.122355 to 0.11297 WARNING: damped steplength 0.130429 to 0.11297 WARNING: damped steplength 0.190782 to 0.11297 WARNING: damped steplength 1.96508 to 0.11297 WARNING: damped steplength 1.96508 to 0.11297 WARNING: damped steplength 0.166109 to 0.11297 WARNING: damped steplength 0.548971 to 0.11297 WARNING: damped steplength 0.248398 to 0.11297 WARNING: damped steplength 0.189787 to 0.11297 WARNING: too small "scale" at Newton2NumLineSearch
Should I use these molecules for virtual screening or not because their geometry isn't good? Anyone has some suggestions? Thank you and regards.
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