Re: [Open Babel] Error handling with smi file in pybel?

Hi, That SMILES-string doesn’t look valid. You have half the six-membered ring specified as aromatic and the other half as aliphatic. It seems like AddHydrogens is fixing this and adds hydrogens to match up the “aromatic” carbons. Med vänliga hälsningar, Fredrik On 11 Sep 2019, 20:41 +0200, S

[Open Babel] Problems with MOL2->PDBQT Conversion

I have noticed that when I convert MOL2->PDBQT that in some cases the bonds and protonation of the molecule are changed. I am including two such examples. Thoughts? thanks, Scott mol3_core.pdbqt Description: Binary data mol2_core.pdbqt Description: Binary data mol2_core.mol2 Description:

[Open Babel] DIFFICULTIES CONVERTING COMPOUNDS TO A DIFFERENT FORMAT

Dear Team, Thank you very much for providing such a wonderful program to help make research and studying easier. I have been trying to get a Protein Data Bank (pdb) Files Format for an analog compound that was designed on free Trial version of PerkinElmer's ChemDraw Professional to use in a dock