# How to Perform point mutations with NCAA

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How to Perform point mutations with NCAA
#1

Hello Everyone,

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.

Post Situation:
Tue, 2021-06-22 02:05
Subhrodeep Saha

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:

37 A PIKAA X[DORN]
Thu, 2021-06-24 13:23
vmulligan

When I tried to run old ncAA design tutorial with rosetta_bin_linux_2021.16.61629_bundle, it failed with

• ERROR: Error in ResfileContents::check_for_deprecated_commands(): The "NC" command has been deprecated.  Please refer to the documentation on PackerPalettes (https://www.rosettacommons.org/docs/latest/rosetta_basics/structural_concepts/PackerPalette) for details on how to properly use PackerPalettes to create a set of ResidueTypes with which one will design, and TaskOperations to prune away ResidueTypes that are not desired at a particular location.

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?

best,

Doo Nam

P.S.

However, I prefer to use RS (who wouldn't?) for more organized/faster running.

File attachments:
Fri, 2022-04-22 17:00
dnamkr