I am working on using the application pepspec to identify possible peptides that would bind to a protein of interest but am running into significant difficulties at the actual peptide generation stage.
After running anchordock with three other homologous proteins in order to generate a good estimate of the anchoring residue, I
use the anchor dock output (pdbs, cst files) as input to the pepspec application. The results that I get make no sense as it just outputs pdbfiles with the correct anchor, but with the other residues not connected to the anchor and spread out around the protein structure.
I've ran the pepspec demo, using the provided inputs and have gotten similar results. I guess my ultimate question is whether anyone else has experienced this? I am new to rosetta and running version 3.4, I have not been able to try this on any earlier versions yet. I have attached pictures of the pepspec output pdbs for further clarification
Just as an update, I downgraded to Rosetta 3.3 and the same inputs have been working well. It seems like something got broken in this particular application in the upgrade
I am experiencing the same issue, for both versions 3.4 and 3.5.
Will try to use 3.3!
I can't comment on 3.5, but dr. Chris King had sent me this patch for pepspec for 3.4 earlier, and it had fixed an issue similar to what you're describing, so maybe try compiling with it? Do backup stuff, though.
If you're trying it, rename the file in the attachment to pepspec.cc and replace the original pepspec.cc file, then re-compile Rosetta.
Good luck. :)
Chris King has informed me that the issue should be fixed, and from what I can tell the fix should be included in the 3.5 release.
If you're still having problem with pepspec with Rosetta 3.5, please provide further details, as it's likely a different issue from the one encountered by rrphenix in Rosetta 3.4.