I am trying to dock dNTPs into HBV RT by means of BSP-SLIM. I converted PDB formats into SDF via the SMILES translator. Without additional editing the dNTP.sdf files are looking well in both Chimera and Pymol. Any editing (removal of header lines and/or removal of anything between M END and $$$$) disturbs display by Chimera and/or PyMol (Pymol notes "improper atom count"). After cleaning (header removal and adaptation into M END $$$$), I cannot see a difference with the example.ligand.sdf, but in contrast, my files do not display in Pymol and/or Chimera nor run properly in BSP-SLIM. I attached one of them in SMILES translator (SDF - 3D) output format with a txt extension. What is wrong?
Thanks in advance,
Formijn J. van Hemert