[Avogadro-Discuss] amino acid residue atom names

[Grange H. <ghe...@po...>]

Hi, for the suggestion box:

(1) When I save a built peptide as PDB, the atoms don't have the expected names i.e. CA, CB, HG12, ND2 ...
It is vital that they do. Quantum chemistry packages haven't previously been interested in these, but will soon do so. Quantum Chemistry on GPU (TeraChem) will take PDBs directly as input, and residue atom names will not be lost.
(2) When building peptides, there are a number of things it would be nice to have:
be able to specify Acetyl and NMe caps;
be able to specify 3-10 and pi helix in addition to the existing conformation types (though can in effect already do so by specifying suitable default phi and psi).