After using the flag -icoor_05_2009 in Flexpepdock refinement it can't recognize acetylated lysine residue (ALY).
What is purpose of using this flag and how to make it to recognize ALY residue if possible?
NOTE TO NON-DEVELOPERS: Talaris 2013 is the "new standard" Rosetta scorefunction, to replace score12. It's not released yet.
The purpose of the icoor flag is to "fix" some of the internal coordinate errors in the fa_standard residue type set. I forget what they are; the only error I can remember off the top of my head is that cysteine CB is in the wrong place, and some of the hydrogens have weird angles.
The fa_standard residue type set has five-plus years of development and enrichment with noncanonical residue types, patches, etc. ALY is one of those patches. Nobody has ported those patches and noncanonicals and post-translational modifications over to the icoor residue type set. Since you need it, congratulations, you've just been volunteered!
Compare the files in
Rosetta/main/database/chemical/residue_type_sets/fa_standard (particularly patches/lys_acetylated.txt)
You need to port lys_acetylated into the icoor set. Make sure that it is consistent with any changes to lysine between fa_standard and the icoor (there are many, but I don't know what they mean).
I looked at the param files and in icoor there is an extra column present for ATOM along with some other changes. I have no previous knowledge regarding param files, but I will be happy to create the patch file. Could you please suggest me some useful info available regarding this?
Nawsad, I would contact Jason Labonte - JWLabonte@jhu.edu - He should be able to help. He would also probably be interested in writing a python class/script to do it automatically for all fa_standard params if possible. He has created a lot of params/patches for getting Rosetta to understand carbohydrates.
Thanks for the reply. I will be glad to get help from Jason. Please let me know if you hear from Jason regarding this.
If you're talking about the sixth column in the ATOM line (the one after the partial charge column), that's the PARSE charge column. (PARSE charges are a different partial charge scheme.) It's completely optional. If you don't give a PARSE charge, it will just use the regular partial charges. Besides, they will only be used if you specify the -corrections:chemical:parse_charge flag.
The reading of params files are entirely identical between the fa_standard and fa_standard_05.2009_icoor directories. (In fact, *all* params files go through the same loading code.) You should be able to copy a file into the directory, update residue_types.txt and have your new residue be working.
Hi Rocco !
Thanks for making the six column part clear to me.
Isn't it right the patch files for fa_standard_05.2009_icoor should be different from those in fa_standard and it should be consistent with changes to residues between fa_standard and fa_standard_05.2009_icoor? As Steven mentioned earlier there are many and it should be taken care of.
The format (syntax) of the patch files should be the same (again, they go through the same interpreter, regardless of directory). Whether there should be any numeric differences in parameters, I don't know. Absent any indication otherwise, I would doubt it. If I recall correctly, the main difference between the directories (aside from the parse charges) is small differences in the ideal bond lengths/angles in the icoor lines. That shouldn't affect any of the settings in the patch files, or if it does, it would be in a non-systemic fashion which would require a concerted level of testing/benchmarking. (Akin to the effort which lead from the fa_standard to fa_standard_05.2009_icoor transition.)