1) Are backbone parameters different for different amino acids?
Yes, in some AMBER FFs, there may be differentiation between different CA atoms.
2) Should we fully perceive all backbone parameters and SMARTS, or should we define a minimal number of SMARTS by hand?
Approaches:
Iterate over all tripeptides and filter for parameters with backbone atom types (will yield 675 combinations with lots of redundancy) -- Will need to spin up CHEMPER/SMIRKY to collapse these patterns down to minimally differentiated SMIRKS
Just know how many unique backbone parameters there are and write them by hand
Seems like we aren't certain enough in our knowledge to do the latter, so we should pursue the former.
Backbone parameters
1) Are backbone parameters different for different amino acids?
Yes, in some AMBER FFs, there may be differentiation between different CA atoms.
2) Should we fully perceive all backbone parameters and SMARTS, or should we define a minimal number of SMARTS by hand?
Approaches:
Seems like we aren't certain enough in our knowledge to do the latter, so we should pursue the former.