I would like to ask you about computations of a change of stability, 'ddG = dGmutant ‐ dGwildtype'. I use Rosetta for the very first time. I employ Rosetta 3.9.
I have adjusted our crystal structure 'structure.pdb' by MolProbity (addition of hydrogens) and by the Rosetta program 'clean_pdb.py'. The file structure.pdb is not minimized/optimized/relaxed.
I have prepared input.mutfile for 30 single mutations in this way:
R 60 Q
E 62 K
but I am not sure whether it is correct.
'High-Resolution Protocol Flags' is convenient for my purpose, therefore, I have copied the options from https://www.rosettacommons.org/docs/latest/application_documentation/analysis/ddg-monomer to a flags file.
Unfortunately, I do not understand how to set some options.
According to comments on the options, I think that minimization can run by these default settings without other keywords:
Is it correct?
A similar problem lies in a preparation of a constraint file. According to the section Algorithm (the link above), it is possible to choose an automatically generated file, which I prefer, but I do not know how to set it. If the keyword 'ddg::min_cst true' automatically makes the constraint file does it mean that the keyword is only '-constraints::cst_file' so without a name specification?
And my last question is how to run it in the command line with and without flags file? I have found this link https://www.rosettacommons.org/manuals/rosetta3.1_user_guide/app_ddg_prediction.html where all options are explicitly put in the command line but I do not understand how to work with flags.
Would you be so kind as to help me, please?
Thank you in advance for your answer.