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Hi!
I have a peptide which has nonstandard amino acid NAL at the N-terminal and C-terminal, and I want to use CHARMM36 force field to generate it’s parameters, there are no dihedral parameters composed by NAL and N-terminal or C-terminal in the force field; However, when the NAL in the middle of the peptide, it has parameters. So, why does the NAL have no parameters when it is at the N and C ends?
Which dihedrals are specified on those lines? I’d guess they are related to φ’ and ψ’ and thus depend on Cβ. Residues are typically developed as capped dipeptides so there may not be parameters for these species at termini, but they could likely be copied from chemically analogous groups.
Thank you for you answer!
The two missing dihedrals are NH3-CT1-CG321-CG2R611 at N termini and CC-CT1-CG321-CG2R61 at C termini. Which dihedrals are suited for replacing?
Otherwise, I would like to know the φ’ and ψ’ stands for which angles and Cβ stands for which atom in my structure?
Thanks!
These are not relevant, they were only a guess on my part. Your issue arises from χ1 definitions related to terminal amino acids.
CB (beta carbon)
The equivalent parameters (at least by analogy) that you could import for your missing dihedrals will come from PHE, so NH3-CT1-CT2-CB and CC-CT1-CT2-CA.
Thank you!
