EDIT: I would like to flag that I am a commercial user so a timely response from the developers would be greatly appreciated.
Hello Folks,
I would like to run PIPER-FlexPepDock for blind docking of a short peptide ligand to a receptor.
I am following the tutorial (https://www.rosettacommons.org/docs/latest/application_documentation/docking/flex-pep-dock) but can not find a number of the required applications including "pdbprep.pl", "pdbnmd.pl", and the main piper application "piper.acpharis.omp.20120803" in "rosetta.binary.linux.release-362".
I have noticed a number of unanswered questions on this topic: https://www.rosettacommons.org/node/10701
After further investigation I worked out that PIPER is not distributed with Rosetta and is instead part of the Schrödinger suite of software (https://newsite.schrodinger.com/platform/products/piper/; and requires a separate commercial licence).
Is there still a method for peptide docking available in Rosetta (no server suggestions)?
Kind regards