The Molecular Graphics Laboratory Forum

I am interested in generating 2D representation of my docking results using Poseview.

I looked at the FAQ section on how to save the protien-ligand complex as PDB format. The file it generates is actually different from from a regular pdb file. While Pymol had no problem loading it, other program such as Babel seem unable to recognize it. I need to convert the docked ligand into sdf format so I can use Poseview.

Anyone knows how to convert the docked result into a real pdb format/ sdf format or any other way to work around it?

Hi desperate4love,

normally I save the docked ligand of interest in a PDB with ADT. (just mark entry and klick save molecule)
After that I bring the pdb of the ligand together with the receptor pdb-file with pymol and save both stuctures to one pbd.

That should give you a working pdb.

Kind regards
cis-peptide