I recently came across the paper titled "Anchor extension: a structure-guided approach to design cyclic peptides targeting enzyme active sites" and wanted to try it out for myself. I downloaded the supplemental materials and tried to follow along the READMEs to test out Methods 1-4. But I am not able to actually get any of them to work even with the provided pdbs. Is anybody else having the same problem?
Here is what I have tried...
For Method 1, I set up a conda environment for python2.7 and ran python ../main.py -f target.pdb --targetresidues "ALA 3" -q 8mer_ALA.pdb --queryresidues "ALA 370" which generated the realign8mer_ALA.pdb. So far so good.
I then edited the merge_8.xml script to use realign8mer_ALA.pdb and tried to run it and It gave me the first error in crash log.
I also tried adding the flag -input_empty_pose true as a flag and tit gave me the second error in the crash log.
I am attaching the xml file (as a txt) in case it was something silly and obvious.
Has anyone been able to get this to run?