I am running foldx position scan for GFPmut2 (PDB: 6GO9) and I use a config file with the following template:
command=PositionScan pdb=6GO9.pdb pdb-dir= <pdb location> output-dir= <output directory> output-file= <file name> positions= <list of positions, comma separated: QA204R,KA107R...>
I had created three different config files with different position list.
Some of the positions were present in more than one files. Foldx produced different estimates of ΔΔG for these positions from these different config files. Example:
File1-LYSA41K 0 File1:LYSA41R -0.353758 -- File2-LYSA41K 0 File2:LYSA41R -0.0356187 -- File3-LYSA41K 0 File3:LYSA41R -0.0031362
File1-LYSA52K 0 File1:LYSA52R 0.0057333 -- File2-LYSA52K 0 File2:LYSA52R -0.00809613 -- File3-LYSA52K 0 File3:LYSA52R 0.0077189
I can certainly run foldx with a union of the three list of positions but I don't understand how this difference can even occur. Shouldn't each position scan be independent?