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.

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