I am trying to mutate multiple residues of a peptide with NCAA to determine their structure and ΔΔG of mutation on Rosetta.
I would be grateful if anyone could share any research article, material or guidance to proceed on this matter.
P.S. - I am a beginner at Rosetta without any bacl ground in coding or bioinformatics. Any help and advice is appreciated.
The simplest thing would be to use the MutateResidue mover in RosettaScripts (https://new.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/MutateResidueMover).
For DDG values, I think the ddg_monomer application (https://new.rosettacommons.org/docs/latest/application_documentation/analysis/ddg-monomer) will work if you do the following. Note that I haven't tested this, though:
1. Add a packer palette that includes your noncanonical using the -packer_palette:extra_base_type_file commandline option. (See https://new.rosettacommons.org/docs/latest/rosetta_basics/structural_concepts/PackerPalette#usage_command-line-applications).
2. Provide a resfile that specifies the noncanonical using the "X" notation. (See https://new.rosettacommons.org/docs/latest/rosetta_basics/file_types/resfiles#commands_commands-for-noncanonical-residue-types). For example, to introduce a mutation to D-ornithine at position 37, it would be:
When I tried to run old ncAA design tutorial with rosetta_bin_linux_2021.16.61629_bundle, it failed with
Therefore, I tried to use PackerPalettes that Vikram mentioned above with CustomBaseTypePackerPalette.
However, RS example in this CustomBaseTypePackerPalette doesn't work even after I commented out terminal_bond1, terminal_bond2 (since these are not defined in movers) with attached error message.
Can any of you (Vikram, Doug, Kevin) upload any simplest toy example of rosetta_script.xml and resfile that run with a fairly recent rosetta version?
Fixbb for ncAA with packer_palette:extra_base_type_file ran well.
However, I prefer to use RS (who wouldn't?) for more organized/faster running.