Enzyme Design

Hello, 

Recently, I had a chance to see a presentation about coupled_moves. There is hardly any information about it since the paper isn't published yet but I figured I would give it a try anyway. What I want to do is to redesign enzyme specificity for a new substrate . The problem is including rotamers library of my new substrate. 

I created ligand rotamers with Frog2 (no acces to MOE or OpenEye) and created params files with:

"molfile_2_params.py rotamers.mol2 --conformers-in-one-file".

Hi everyone,

I am doing enzyme design using a cst file and it seems that my constraint file is not properly defined.
I wish to define constraints such that the peptide N forms hydrogen bond with my ligand in the binding pocket. At the same time I would like this residue to be any other residue except proline. So i defined my cst as follows;

CST::BEGIN
TEMPLATE:: ATOM_MAP: 1 atom_name: O8 P1 O7
TEMPLATE:: ATOM_MAP: 1 residue3: EY1

TEMPLATE:: ATOM_MAP: 2 atom_type: Nbb
TEMPLATE:: ATOM_MAP: 2 residue1: ACDEFGHIKLMNQRSTVWY

Hi everyone,
First of all thanks you for the replies to other post as that has helped me to progress on using Rosetta.
I have generated structures using enzyme design but I am struggling to understand the energy scores.

Hi everyone,

I see some strange behavior of enzyme design with ligand.
1) I have created a library of rotamers, set path to this library in params file (by PDB_ROTAMERS rotlib.pdb) and run enzyme design. But there is still only translation and rotation of rigid body in the active site and no using of the rotamer library. Only when I start with ligand structure with some clashes in the protein pdb file I can see optimization of of torsion angles of the ligand. Can you please explain how it works?