NMR Refinement and Peptide Folding Using the GROMACS Software

27 January 2021, Version 1
This content is a preprint and has not undergone peer review at the time of posting.


Nuclear magnetic resonance spectroscopy is used routinely for studying the three-dimensional structures and dynamics of proteins. Structure determination is usually done by adding restraints based upon NMR data to a classical energy function and performing restrained molecular simulations. Here we report on the implementation of a script to extract NMR restraints from a NMR-STAR file and export it to the GROMACS software. With this package it is possible to model distance restraints, dihedral restraints and orientation restraints. The output from the script is validated by performing simulations with and without restraints, including the ab initio refinement of one peptide.


Molecular Dynamics
Nuclear Magnetic Resonance

Supplementary weblinks


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