I am trying to design the binding site of a protein with certain ligands and there is a common error that I encounter with various ligands (not all). The error says "Angle constraint: 0-length bonds". I checked the input structure and there are no atom clashes. I am not sure what is causing this error. If anyone has an idea, it would be a great help.
Thank you !
If you know that none of your atoms are on top of each other, one thing to do is to double check your constraint definitions. If you accidentally repeated an atom in a constraint definition, then you'll have a zero length bond from the atom onto itself, and that can lead to such an error.
The other thing to consider is if the bonds are not starting off as zero length, but are becoming zero length during sampling. Double check your ligand conformers to see if there are any odd or broken conformers.