Enzyme Design

Hi,

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 !

Purvi

Hi Folks,

I've been playing with the enzyme design binary application using enzymes containing DNA or RNA in the pose. The FlexBB protocol can be activated by setting the flag '-enzdes:flexbb_protocol true'. If no loop file is provided via the flag '-enz_loops_file <file>' the default  protocol behavior is to iterate through the pose to identify flexible regions in the structure for loop design. I found that having either DNA /RNA  in the pose triggers the following error consistently after cst minimization. 

Hi,

I am working on Rosetta Enzyme Design Application trying to design a protein with a particular ligand in desired geometry. I wanted to define a bridged hydrogen bond interaction between the carboxylate group on the ligand and the arginine residue in protein via water molecule.

Hi everyone,

I am currently checking mutations of some key residues in the substrate binding pocket. So far, I used pymol wizard to automatically iterate all 20 amino aicds mutations from position and then use rosetta minimizer to optimize the local energy. 

Since I only change a few residues of the protein, is there any ways that I can only minimize a few positions instead of minimization of whole protein?

Thanks,

Ronghai