I am trying to dock a D- peptide on a protein dimer using the FlexPepDocking application. After collecting all the information I could find from tutorials and old posts I followed the steps described below:
1. I uncommented all the lines under "D-CAA TYPES" in file: rosetta_database/chemical/residue_type_sets/fa_standard/residue_types.txt
2. Downloaded the rotamer libraries from http://carl.bio.nyu.edu/%7Erenfrew/ncaa/ncaa_rotamer_libraries.tar.gz and placed the files inside
rosetta_database/rotamer/ncaa_rotlibs. I did not modify the residue parameter files (*.params) since I noticed that they already included "NCAA_ROTLIB_PATH" and "NCAA_ROTLIB_NUM_ROTAMER_BINS" directives at the bottom.
3. Placed the D-peptide near the binding cavity, assigned chain A to the receptor dimer and chain B to the D-peptide and named the residues of the D-peptide as DILE, DGLN, etc. Here 's a line from the .pdb:
ATOM 1 N DILE B 1 24.948 37.276 -1.105 1.00 0.00 N
4. Added the flag "-score::weights mm_std" in the pre-pack and refinement steps to use the pure molecular mechanics scoring function.
Below are the prepack flags:
And the refinement flags:
Both stages were completed successfuly, yet I am not sure if Rosetta used the D-CAA rotamers and parameter files. Does anyone know how I can find this out? I have also attached the output.
Is there anything wrong with my workflow? Any alternative scoring function I could use?
I would appreciate your comments. Thanks in advance.