Hi there,
Thank you for the information, although I was able to get all of this to work by renumbering the second protein so that it picks up where the first lets off. This allows me to specify the two proteins for docking, and allows me to specify which loops from protein 1 and/or protein 2 that I want to flex during docking.
One thing I have learned is that in order to use -pose -loop during docking, is that one must submit a .fasta sequence containing both the protein 1 and protein 2 sequences when generating fragment libraries. This is not obvious. In addition, those sequences must be continuous (as if there were 1 sequence) and the number of residues in this “single” sequence must correspond exactly to the number of residues in the .pdb file.
It’s only taken me two weeks to figure all of this out 