Thursday, January 2, 2014

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.

=== ===

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:

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
The FragBuilder Python library can be found at GitHub:

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