Protein Mutations File

To set up a protein residue mutation FEP calculation, you can use the FEP Protein Mutation Panel or the Protein FEP for Ligand Selectivity Panel. If you write the job files, a file mutations.txt is created, containing the list of mutations to perform. You can edit this file to add or change the protein residue mutations. Each line contains one or mutations that are performed simultaneously.

A single mutation is specified in the following format:

CHAIN:NUMBER->TARGET

where CHAIN:NUMBER describes the wild-type residue that is mutated, and TARGET specifies the residue, to which it is mutated, in 1-letter or 3-letter code. For ligand selectivity calculations, you can specify multiple mutations within one perturbation by modifying the mutations.txt file.

If you want to perform multiple mutations from the wild type without generating intermediate single mutations, use a space-separated list.

For example, the mutation list:

A:11->LYS A:15->ALA A:21:ALA

generates a single perturbation, simultaneously mutating residues 11, 15, and 21 of chain A.

If you want to generate intermediate mutations, use a comma-separated list.

For example, the mutation list:

A:11->LYS, A:15->ALA, A:21:ALA

generates 6 intermediates in addition to the triple mutation and 12 perturbations in total.

After modifying the mutations file, you can pass it to the fep_plus command using the -protein option.