I have been stuck on the problem of generating rotamer libraries for a while now as I try to repeat the process for non-canonical residues (starting with the test case of ornithine [C40]). The original documentation for this process is provided at the following address:
Some of the commands, as well as flags for the executable have changed since the original demos and the publication that generated this work, so I had to work out a new command line option that is written as follows:
/scratch/Rosetta/demos/public/make_rot_lib/outputs$ /scratch/Rosetta/main/source/bin/MakeRotLib.default.linuxgccdebug -database /scratch/Rosetta/main/database
Running this, however, produces the following error:
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
protocols.make_rot_lib.MakeRotLibJobInputter: Instantiate MakeRotLibJobInputter
terminate called after throwing an instance of 'std::length_error'
Aborted (core dumped)
I played with the make rotamer input file (attached), and nothing seems to make a difference. This same error always occurs.
Adding addition flag options as have been suggested in other online reports about these problems have only yielded larger and more complex errors.
Other attempted fixes include moving the C40.param file to directory:
But if I try to call it directly:
I get an exception:
[ERROR] EXCN_utility_exit has been thrown from: src/core/scoring/ScoreFunction.cc line: 2679
ERROR: Unable to open weights/patch file. None of (./)talaris2014 or (./)talaris2014.wts or
If there is anyone who has managed to actually produce rotamer libraries using Rosetta3 and can tell me what my commands are missing, or if you can provide me with some sample files that are able to function properly, I would really appreciate the help.
This problem has held me up for quite some time and I am really hoping someone has been able to make use of this protocol (or an alternative protocol that can make non-canonical residues like alpha-amino acids and peptoids) since it was published.