I am having a problem when setting the packer to design residues that are non canonical in the pdb file I provide. I have an example for 2ovq where the short peptide called chain C has two phosphorylated residues (TPO at 380 and SEP at 384). When I make a resfile like this:
384 C ALLAA
The packer will only sample this position with phophoserine, phosphothreonine or phosphotyrosine. My interpretation is that the packer is secretly aware of the class of modified residues and only considers the phosporylated residues as "canonical" replacements for this class. I am experiencing the problem running the ddg_monomer application but it seems to be a feature of the packer and not the app.
Question is then; how can I turn this off? I want the packer to sample all the residues that we normally know as canonical (ACFGILM ... ).