| Re: Computational Chemistry [message #629 is a reply to message #628] |
Tue, 17 September 2019 16:44  |
nbehrnd
Messages: 224
Registered: June 2019
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Senior Member |
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Dear ruthamcau,
the single-letter abbreviation in your example is used by the Fasta
format [1]. This is one of the file formats openbabel [2] 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 [3] 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 [4] and the more general introduction to Python
for Bioscientists by Ekmekci et al. in PLOS Computational Bioploy [5,
openaccess] (e.g., exercise #10).
Good luck,
Norwid
[1] https://en.wikipedia.org/wiki/FASTA_format
[2] http://openbabel.org/wiki/Main_Page
[3] http://avogadro.cc/
[4] https://biopython.org/
[5] https://doi.org/10.1371/journal.pcbi.1004867
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