This is the workhorse of FoldX mutation engine. This command ensures that whenever you are mutating a protein you always move the same neighbours in the WT and in the mutant producing for each mutant PDB a corresponding PDB for its WT (each mutation will move different neighbours and therefore you need different WT references). Build model requires a mutant-file to run. The minimal configuration file for BuildModel:
command=BuildModel pdb=BM.pdb mutant-file=individual_list.txt
It can be run using the command line:
FoldX --command=BuildModel --pdb=BM.pdb --mutant-file=individual_list.txt
The parameter numberOfRuns tells the algorithm how many times it should do the specified mutations. Normally it should be set to 1. However, sometimes it can be set to higher numbers (typically 5) to see if the algorithm has achieved convergence, or in other words if the solution offered is the optimal or a trapped solution. The option out-pdb is setted to true by default and can be use with commands as Pssm or PssmStability.
FoldX uses output-file as a tag to label different outputs from different commands in batch runs. After running BuildModel you'll get three files to look at. Given pdb=PDB.pdb the output files are.
- Average_PDB_BM.fxout -> average energy of the different runs
- Dif_PDB_BM.fxout -> energy difference between reference WT and the corresponding mutant
- Raw_PDB_BM.fxout -> full energy decomposition for the WT references and the mutants
- PdbList_PDB_BM.fxout -> names of all the mutants and the corresponding WT references
Output files contains the Gibbs energy of protein folding decomposed into the different terms used by FOLDX. The files Dif_, Average_ and Raw_ have same headers with the energy terms decomposition in Kcal/mol, the colums are: