FragBuilder: Setting up a scan of peptide conformations.

This post covers the essentials of how to set up a scan of different peptide conformations. We have used this method to calculate more than 1.5M QM calculation on model peptides in our group.

In this example we make a tri-glycine peptide and scan over the phi/psi torsion angles between -180 and 180 degrees with 60 degrees spacing.

For each conformation, the MMFF94 force field energy is printed and the structure is saved as an XYZ file.

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FragBuilder: The paper is out (as preprint)!

Our latest papers on the FragBuilder Python library is out as preprint from PeerJ, while it is undergoing peer-review.

PeerJ is in my opinion awesome for this type of publications, demonstating the use of a Python library, since they even allow examples and code-bits in the paper.

You can see the preprint here: https://peerj.com/preprints/169v2/

We even got DOI and can be cited as:

Christensen AS, Hamelryck T, Jensen JH. (2013) FragBuilder: An efficient Python library to setup quantum chemistry calculations on peptides models. PeerJ PrePrints 1:e169v2 http://dx.doi.org/10.7287/peerj.preprints.169v2

The FragBuilder Python library can be found at GitHub: https://github.com/jensengroup/fragbuilder

I am in the process of making a couple of more blog-posts to demonstrate the use of FragBuilder, stay tuned!