Mutates selected positions to a list of provided residues and, after that, calculates the DDG of interaction energy upon mutation. The defaults are set to the 20 "natural" aminoacids. It makes use of BuildModel to mutate the residues and AnalyseComplex to calculate the interaction energies. This is an example of how the new implementation of FoldX can create complex commands by combining the basic ones. The minimal configuration file for Pssm is:


It can be run from the command line:

FoldX --command=Pssm --analyseComplexChains=A,B --pdb=PM.pdb --positions=GA5a,GA14a

FoldX uses pdb as a tag to label different output in batch runs. After running Pssm you'll get one file to look at. Given pdb the output file is:

  • PSSM_pdb.txt -> average energy of the different runs

Pssm also produces all the outputs related to the BuildModel and AnalyseComplex commands that, combined, give rise to the Pssm command.



Parameter Description Default value
aminoacids Residue list for pssm in string format ACDEFGHIKLMNPQRSTVWY
analyseComplexChains all
clashes get the PSSM clash matrix false
moveNeighbours set to move neighbours when we mutate true
numberOfRuns set the number of runs done in BuildModel or DNAScan 1
out-pdb set to output PDBs when doing mutations true
pdbDummys output the the dummy atoms we use (for N and C caps of helixes as well as the free orbitals) in the generated pdbs false
pdbHydrogens output the hydrogens we place in the generated pdbs false
pdbIsoforms output the isoforms of the His in the generated pdbs false
positions positions to do mutagenesis for PosScan or Pssm