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CIF2gromacs-2.pdf (248.35 kB)

NMR Refinement and Peptide Folding Using the GROMACS Software

preprint
submitted on 25.01.2021, 16:57 and posted on 27.01.2021, 11:21 by Anna Sinelnikova, David van der Spoel

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.

Funding

TheSwedishresearchcouncilisacknowledgedforagrantofcomputer time (SNIC2019-2-32 and SNIC2020-15-67) through the National Supercomputing Centre in Link ̈oping, Sweden. Funding from eSSENCE - The e-Science Collaboration (Uppsala-Lund- Ume ̊a, Sweden) is gratefully acknowledged. The authors would like to thank Snehal Patel for stimulating discussions. A.S. acknowledges funding from the Knut and Alice Wallenberg foundation through the Wallenberg Academy Fellow grant of J. Nilsson.

History

Email Address of Submitting Author

David.VanderSpoel@icm.uu.se

Institution

Uppsala Universitat

Country

Sweden

ORCID For Submitting Author

0000-0002-7659-8526

Declaration of Conflict of Interest

There is no conflict of interest

Version Notes

Submitted for publication.

Exports

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