** note: these script call on OpenEye tools, particularly openeye.oechem openeye.oeomega openeye.oequacpac openeye.oeszybki ** thus a valid OpenEye license for these tools is required
1.) create a SMILES string of your amino acid that has an acetyl group added on to the N-terminus and an N-methyl group added to the C-terminal end
aspartic acid example:
O=C(NC)[C@H](CC(=O)[O-])NC(C)=O
2.) run the "charge_and_correct.py" script, providing the following inputs: text file with the amino acid SMILES string total charge of side chain three letter identifier
python charge_and_correct.py --smiles test.smi --charge -1 --aa_name ASP &> ASP_torlib_OE
this will generate a mol2 file with partial atomic charges and some footers needed for step 3 also, pipe the output to a file to be used as input to step 4
3.) run molfile_to_params_polymer_ARL.py to create .params file for amino acid
python molfile_to_params_polymer.py --clobber --polymer --no-pdb --extra_torsion_output --name ASP ./ASP_AM1BCC.mol2
this generates the .params file that is used on the Rosetta command line to load a new amino acid topology it will also generate a XXX.atom_map file needed for step 4 you may use the --extra_torsion_output file to generate constraints for the side chain depending on your intended use in Rosetta
4.) run the make_rotlib_phi_psi.py script for each phi/psi combination
this requires the ASP_torlib_OE file generated in step 2 in addition to other outputs from previuos steps so it is important to maintain the same 3-letter code for your amino acid
python make_rotlib_phi_psi.py -n ASP --phi -180 --psi 180
this script will also add two lines to the end of your .params file adding information about the number of idealized chi values in addition to the location of the final rotamer library
5.) once all of the individual rotamer library files are generated for each phi/psi combinationn, combine them all into the final rotamer library with the "make_final_rotlib.py" script
python make_final_rotlib.py -n ASP