I would like to define a potential between the CB atoms of a certain pair of residues in both centroid and full-atom refinement steps during Abinitio protocol. While in full-atom representation there is no ambiguity, I was wondering if the position of the CB is represented correctly in the centroid mode or this position would be the center of mass of the "super-atom" that represent the side chain, for example. If is not the first case scenario, would it be possible to calculate was it the difference between the "actual" position of CB-like atom in the centroid mode and the position it will be present in the full-atom representation? (I imagine it is a constant...).
ps. I know it would be an alternative to define in terms of CA atoms, but defining in terms of CB atoms implies an aditional accuracy to the potential.
~/ROSETTA/Rosetta/main/database/chemical/residue_type_sets/centroid/residue_types/l-caa hosts the centroid parameters files. You will see that CB atoms are present in these parameters. I spot checked a few and the CB position was similar to where it is in the fullatom params. I expect CB is essentially correct; its sterics are important for ramachandran, after all.
That is good news!
Is there a place where I can access what is the meaning of each of those parameters? I mean, a description of the file... Right now, I am trying to infer them.
The params file format is older than 2007, which is a roundabout way of saying no.
I'm ignoring the other fields but can attempt to answer a specific question.
ooh, someone did write it. It's in-code at source/src/core/chemical/residue_io.cc in a big comment midway though the file.
Pasting from the developer chat:
"Yeah, the docs in that file are the best description of the params file. There is also some high slightly higher level discussion in the Drew et al. NCBB paper (http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0067051)"
Thank you smlewis!
I will take a look. It was of a great help!