Hi Chengxin,
Happy New Year!
Thanks for the earlier tip. I would like to reproduce your FoldX4 results exactly so I can compare to my method. As suggested I paraphrased your commands from runFoldX.py. This gave me:
cd /proj/nobackup/BindProfX.0ps.3/1A22/B-327-A-test
cp /proj/nobackup/XBindProfPaperData/pdbs/1A22.pdb ./raw.pdb
echo "EB86A;" > individual_list.txt
/home/samuelf/local/foldx4-2017/foldx --command=RepairPDB --repair_Interface=ONLY --pdb=raw.pdb
/home/samuelf/local/foldx4-2017/foldx --command=BuildModel --pdb=raw_Repair.pdb --mutant-file=individual_list.txt
/home/samuelf/local/foldx4-2017/foldx --command=AnalyseComplex --pdb=raw_Repair_1.pdb --analyseComplexChains=A,B > mutant.out
/home/samuelf/local/foldx4-2017/foldx --command=AnalyseComplex --pdb=WT_raw_Repair_1.pdb --analyseComplexChains=A,B > WT.out
Kindly let me know if I parsed your program correctly. The issue is that your DDG for this mutant (1A22.pdb, cleaned mutation string EB86A) was 1.3931. I am getting +0.18:
tail mutant.out WT.out
Total = -22.68
Total = -22.86
I realize these two values (.18 vs. 1.39) are well within the error bars of the method. Still I feel it is important to get it exactly right, otherwise we could be comparing apples and oranges. As you see I am using this year's FoldX4 rather than 2013's. However for a few reasons I suspect the two are the same.
Thanks
Sam