|Re: Computational Chemistry [message #629 is a reply to message #628]
||Tue, 17 September 2019 16:44
Registered: June 2019
the single-letter abbreviation in your example is used by the Fasta
format . This is one of the file formats openbabel  accepts as
input; available for free, either with a GUI, or to run on CLI / script
with bindings to languages like Python, C++. Beside .xyz and .pdb, the
.txyz for TINKER equally is one of the formats openbabel may write. As
option, openbabel itself may offer /a guess/ about the conformation with
forcefields like UFF or MMFF94 but intended for small molecules.
Avogadro  may be on first sight less interesting for you because it
lacks an export to TINKER, and allowing you to construct via GUI (build
-> insert) peptides by three-letter, RNA/DNA by single-letter buttons.
But under «extensions» you have multiple templates to set up input files
of quite a number of quantum chemical programs; as such complementary
to pure openbabel.
Continuing with a programmatic approach to handle peptide sequences, I
would mention Biopython  and the more general introduction to Python
for Bioscientists by Ekmekci et al. in PLOS Computational Bioploy [5,
openaccess] (e.g., exercise #10).