It is highly recommended to repair your structures before you do any modelling with FoldX. RepairPDB identify those residues which have bad torsion angles, or VanderWaals' clashes, or total energy, and repairs them. The minimal configuration file for RepairPDB is:
command=RepairPDB pdb=RP.pdb
It can be run from the command line:
FoldX --command=RepairPDB --pdb=RP.pdb
The way it operates is the following: First it looks for all Asn, Gln and His residues and flips them by 180 degrees. This is done to prevent incorrect rotamer assignment in the structure due to the fact that the electron density of Asn and Gln carboxamide groups is almost symmetrical and the correct placement can only be discerned by calculating the interactions with the surrounding atoms. The same applies to His. We do a small optimization of the side chains to eliminate small VanderWaals’ clashes. This way we will prevent moving side chains in the final step. We identify the residues that have very bad energies and we mutate them and their neighbours to themselves exploring different rotamer combinations to find new energy minima. FoldX uses output-file as a tag to label different outputs from different commands in batch runs. After running RepairPDB you'll get two files to look at. Given pdb=PDB.pdb the output files are:
- PDB_Repair.fxout -> energies of the repaired residues
- PDB_Repair.pdb -> repaired Pdb
