I have been trying to perform Ligand Docking with the ROSETTA software. I describe what I have done:
1. First, I have the ligands in sdf/mol2 format one per file. I add hydrogens to these and create the params files with the "molfile_to_params.py" script.
2. Second, I clean the protein (no ligands or cofactors) and add H to the protein.
3. Third, I concatenate the protein with each ligand in a different file for each ligand (the ligand has chain identifier X, the protein A).
4. Fourth, I prepare the "flags" and "xml" file (both attached as .txt files). The start_from point is specified since the ligands are not in the binding pocket.
5. Then, I perform the ligand docking with these files for each ligand with these command: $ROSETTA/source/bin/rosetta_scripts.linuxgccrelease @flags -in:file:s protein_ligand1.pdb -in:file:extra_res_fa params_ligands/ligand1.params -parser:protocol ligand_docking.xml
However, the results I get are with ligands having strange bonds (as attached in picture).
Could you point me out what am I doing wrong?
|It is used with the .xml extension, but changed to txt so it can be uploaded.||2.93 KB|