The list of mutations can be setted in two ways. FoldX operates two ways of defining mutations, first Mutant File or Individual List mode. The file with the mutations doesnt need to be in the same folder we are running FoldX but then the full or relative path should be specified.
MUTANT FILE MODE
It should contain the sequences of the mutants in one letter code we want to make. The code will automatically identify the sequence in the pdb and mutate the residues that are different. To use mutant file mode you need to set the variable wildtype to the WT sequence, so you need to be careful to put a sequence long enough so that it does not find more than one target, unless you are working with homopolymers and you want to do the same mutations in each subunit. It is required than the name of the file containing the mutations starts by mutant_file.
Example of mutant file:
GQETSYIEDNSNQN GQETSAILWNSNAN GRETSAILWNSNAN
INDIVIDUAL LIST MODE
In this mode the file individual_list.txt contains the mutations we want to make separated by a comma, in the classical FoldX way (WT residue, chain, residue number, mutant residue). It is required than the name of the file containing the mutations starts by individual_list. Don't include any space on the mutation lines.
Example of individual list:
FA39L,FB39L; LA41F,LB41F; KA42I,KB42I; GA46S,GB46S; AA47V,AB47V; LA48S,LB48S; LA52S,LB52S;