Hi, novice Rosetta user here (so apologies in advance for simple / silly questions).
I have small peptide ligands that I am using in standard grafting / design. This has been relatively straightforward. However, one monkey wrench I'd like to throw into the works would be for the design scripts to use a noncanonical amino acid instead of the corresponding canonical one. For example, instead of tyrosine, design interfaces assuming all tyrosines are phosphorylated, or alternatively, impose acetylation or methylation on certain residues.
I found a forum post here (https://www.rosettacommons.org/node/3556) that mentions writing a "patch" file (in this person's case, lysine covalently modified with retinal). Such an approach looks like it might work for me. I just don't know how to either write the patch file, or incorporate it into the design scripts.
Any help or examples, whether on the above "patch" approach or a more appropriate approach, would be much appreciated. Thank you!