#750 3D atom connectivity error in pdbqt

[Ian Scott]

Ian Scott, iscott@frontier.com, Windows 7, 64-bit

When converting files from smiles, mol, mol2 ,sdf into pdbqt with the generate 3D coordinates active the molecules do not form correctly. Rings are broken and strange bonds form (as viewed in PyRx or Autodock). This problem can be avoided by performing the 3D conversion as an independent step with a different file output file type (e.g. sdf to sdf) and then converting to pdbqt without selecting the generate 3D coordinates option. Therefore, the problem is most likely in the pdbqt 3D coordinate generator.

A example problem smiles string: COc1cc(cc(c1OC)OC)C(C(=O)N1CCCCC1C(=O)OC(CCCc1ccccc1)CCCc1cccnc1)(F)F