I'm trying to convert a single SDF file containing a chemical library of 1000+ compounds into individual PBDQT files to use with AutoDock Vina. I have previously used openbabel to convert individually downloaded SDF's into PDBQT's, and this has worked just fine until now (see first image below).
When trying to separate multicompound SDF's using openbabel, I can obtain inidividual SDF's and PDB's just fine. But when I try to convert to PDBQT, the structure is ruined (see second image below).
I can successfully convert to PDB with correct structure, so I tried to use Reduce to make sure all hydrogens are added to each compound (I thought I read that openbabel might try to recalculate bonds if each atom has an incorrect number). However, when I converted the corrected PDB to PDBQT, the result was the same ruined structure.
Has anyone come across anything like this before? Is there anything I might be missing that could be causing this?