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Issue in the setup.py for non s-s bond system #16

Open xy127 opened 10 months ago

xy127 commented 10 months ago

Hello, Sorry to bother, I'm trying to repeat the CDK2 example in the tutorial folder by following the instructions in the Readme.md. In the third step of seting up FEP, after executing python setup.py, the following error occurs:

 usage: QligFEP [-h] -l1 LIG1 -l2 LIG2 -FF {OPLS2005,OPLS2015,AMBER14sb,CHARMM36,CHARMM22,CHARMM_TEST} -s {water,protein,vacuum} -c CLUSTER [-r SPHERERADIUS] [-b CYSBOND] [-l {1,0.5}] [-T TEMPERATURE] [-R REPLICATES]
               [-S {linear,sigmoidal,exponential,reverse_exponential}] [-w WINDOWS]
QligFEP: error: argument -b/--cysbond: expected one argument

The error is caused by the line 98 in setup.py call = setupFEP + ' -l1 ' + mol1 + ' -l2 ' + mol2 + ' -FF OPLS2015 -b' + cysbond + ' -S sigmoidal -s protein -c TETRA -r 25 -l 1 -w' + windows , where the option -b is empty. I checked the protPREP.log in 2.protprep in which no s-s bond is crearted for this protein. And if I removed the '-b' option, no error would occur. So Is there an 'if condition' missed in the setup.py so that proteins with no S-S bond don't need '-b' option.

Thanks