Dear lab team,
I'm a student in Tel-Aviv university working on the problem of predicting DDG and I'm trying to use your standalone DDG predictor in order to reproduce the reported results of your method.
I downloaded your BindProfX suite, and I was able to run it on your demo directory and obtain results (this time I reinstalled biopython 1.68 as you instructed me to do). I have a problem now when I'm running on the attached data. The problem has something to do with your algorithm not being able to generate the align.out file.
I'm also seeing this output which is unusual:
step 1: iAlign
/home/yotamfr/development/BindProfX.2017-03-04/bin/XBindProf/ialign/ialign.pl -a 2 -n ave -s -minp 7 -mini 7 -dc 4.5 -e is -w /home/yotamfr/development/BindProfX.2017-03-04/bin/XBindProf/lib -l /home/yotamfr/development/BindProfX.2017-03-04/bin/XBindProf/lib/dimer.list X_DiEZvBalYL1bXvoH.pdb >X_DiEZvBalYL1bXvoH.ial
Running from terminal, the program just hangs in the air doing nothing...
In order to reproduce the problem, please run the command:
python2 get_final_score.py XBindProf/1CSE/
with the attached data.
Best regards,
Yotam