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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	from fragbuilder import Peptide
	# Create a peptide object with the sequence
	# glycine-glycine-glycine.
	sequence = "GGG"
	pep = Peptide(sequence)
	# Define a list of angles.
	angles = range(-180, 180, 60)
	# Double loop over phi/psi angles in the desired range.
	for psi in angles:
	for phi in angles:
	# Set the second (leucine) residue to (phi, psi).
	pep.set_bb_angles(2, [phi, psi])
	# Print the energy of the peptide in this state.
	# This is of course just an example.
	print pep.get_energy()
	# Save each conformation.
	pep.write_xyz("pep_%04i_%04i.xyz" % (phi, psi))

view raw make_scan.py hosted with ❤ by GitHub

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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!