- Add the missing side chains using Modeller and can be done in Chimera, but you need to obtain key to access Modeller service online
- Clean the protein i.e, delete solvent and add missing side chains etc using Dock Prep in Chimera by running the following script. The script below also adds hydrogens to the ligand and saves it to ligand_wH.pdb file. Cleaned protein is saved to protein_clean.pdb
- Upload ligand_wH.pdb file to LigParGen server and download the zip file and unzip and keep the files in the same folder
- Make sure you installed Gromacs on your system
- Download OPLS-AA/M protein force field parameters from JorgensenResearch Group page and save it to your Gromacs topology folder.
- Run the following python script