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;
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
CONSTRAINT:: distanceAB: 3.20 0.20 50.00 0
CONSTRAINT:: angle_A: 153.00 20.00 50.00 360.00
CONSTRAINT:: angle_B: 110.00 20.00 50.00 360.00
CONSTRAINT:: torsion_A: -60.40 20.00 50.00 360.00
I also used a resfile which did not affect the residues in the cst file. However, I noticed that this constraint is not respected as the native residue found in the starting pdb is maintained in all designed structures. Is this the correct way to define a hbond constraint formed by any residue?
Thanks in advance for your expert help.
The residue specifications in the constraint file is really only used by the matcher when it attempts to create the constraints. During the actual design portion, the allowable residues are specified by other means.
How exactly that works depends a bit on how you're doing the design run. Which program are you using to do the design, and what's your commandline/script?
find attached my flag file. I am using enzyme design application and my command line is
By default, the behavior of the enzyme_design application is to prevent design at constrained positions - the assumption is that you already sampled the sequence variability at those positions when you did the matching.
There is a special case for backbone constraints, though. What you need to do is add the line
TEMPLATE:: ATOM_MAP: 2 is_backbone
to the appropriate block to specify that this constraint is a backbone only constraint for that residue and that design is permitted at that location.