Dear fellows,
The list of atom types in GenericAtomTypes.md file from Rosetta documentation is not complete. So, I would like to add all necessary properties for some atom types (e.g., amide Nitrogen and deprotonated aromatic Carbon). I have already added their names into molfile_to_params.py scrypt. Now there is a necessity of specification their properties in files on such directories, as ~/Rosetta/rosetta_src_2020.08.61146_bundle/main/database/chemical/atom_type_sets/fa_standard/ and ~/rosetta_src_2020.08.61146_bundle/main/database/chemical/atom_type_sets/fa_standard/extras/. My main question consists in that, how can I find all these numerous parametres. I have already realized that many of these properties may be just copied and pasted from other atoms. Nevertheless, a task of finding a lot of them has still remained an unovercomeable problem for me, such as MEMB_LK_DGREFCE (MEMB is here for ‘Membrane’ or ‘Member’?) as so on and so forth…
What about some Lazaridis-Karplus energy terms, can I rely in data mining on the Lazaridis and Karplus article ‘Effective Energy Function for Proteins in Solution’ for 1999 year (issue – PROTEINS: Structure, Function, and Genetics 35:133–152)? Do dGref(b) and dGfree(c) from Table 1correspond LK_DGREFCE and LK_DGFREE terms, respectively, in the foregoing Rosetta database files?
I am confused whether the term ‘LK_DGFREE’ means Lazaridis-Karplus degrees of freedom or Lazaridis-Karplus free energy?
I attach the lists of heading, these define respective atom properties from the foregoing two folders.
I will really thankful for your response and I am looking forward to it.
Sincerely,
Corvin.
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