SequenceDetail

It prints the sequence information of the protein in a column format: AA, Chain, Pdb Number. The minimal configuration file for SequenceDetail:

command=SequenceDetail
pdb=SD.pdb

It can be run from the command line:

FoldX --command=SequenceDetail --pdb=SD.pdb

FoldX uses output-file as a tag to label different outputs from different commands in batch runs. After running SequenceDetail you'll get one file to look at. Given output-file="TAG" the output file is:

  • SD_TAG.fxout -> sequence information If you don't set output-file

TAG will be the pdbId of the first pdb on the batch.

SequenceDetail energy terms

This is the field description of the output file for the output SD_TAG.fxout in the same order they appear on the file.

Title energy_description
three_letter Three letter residue code
chain Peptide chain of the residue
pdb_seq_num residue number in pdb
omega Ω angle
phi Ø angle
psi ψ angle
sec_struct DSSP information
electro Electrostatic interactions contribution
entrop_mc Entropy cost of fixing the main chain
entrop_sc Entropy cost of fixing the side chain
sideHbond Side chain Hbond contribution
backHbond Backbone Hbond contribution
energy_VdW Contribution of the VanderWaals
energy_SolvP Penalization for burying polar groups
energy_SolvH Contribution of hydrophobic groups
energy_vdwclash Penalization due to VanderWaals’ clashes
sloop_entropy ONLY FOR ADVANCED USERS
mloop_entropy ONLY FOR ADVANCED USERS
energy_torsion Contribution to VanderWaals’ torsional clashes
backbone_vdwclash Backbone-backbone VanderWaals. These are not considered in the total
total Residue contribution to the total energy
cis_bond Cost of having a cis peptide bond
water Residue contribution of water bridges
disulfide Residue contribution of disulfide bridges
energy_dipole Electrostatic contribution to the helix dipole
energy_kon Contribution to electrostatic interaction between molecules in the precomplex
partcov Interactions with bound metals
sc_partcov Side chain interactions with bound metals
energy_sc_SolvH Side chain contribution to hydrophobic groups
energy_sc_VdW Side chain contribution to the VanderWaals
energy_sc_SolvP Side chain penalization for burying polar groups
entr_complex Residue contribution to entropy cost of forming a complex
electroSc Side chain electrostatic interactions contribution
energyKonSc Side chain contribution to electrostatic interaction between molecules in the precomplex
energyIonisation Contribution to ionisation energy
ab_index *