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:
command=Pssm analyseComplexChains=A,B pdb=PM.pdb aminoacids=ACD positions=GA5a,GA14a
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.