Supporting Information for: Parameterization of cholesterol for the Martini 3 coarse grained force field

by Luís Borges-Araújo ¹²; Ana C. Borges-Araújo ¹; Tugba Nur Ozturk³; Daniel P. Ramirez-Echemendia⁴; Balázs Fábián ⁵; Timothy S. Carpenter³; Sebastian Thallmair ⁶; Jonathan Barnoud ⁷⁸; Helgi I. Ingólfsson³; Gerard Hummer ⁵; D. Peter Tieleman⁴; Siewert J. Marrink ⁹; Paulo C. T. Souza ²; Manuel N. Melo ¹

• Corresponding authors: Manuel N. Melo - [email protected]; Paulo C.T.Souza - [email protected]

Cite us!

If you use these parameters please cite the following article: Borges-Araújo, L. et al. Martini 3 Coarse-Grained Force Field for cholesterol. (2023) doi: https://doi.org/10.1021/acs.jctc.3c00547

Contents

This github repository contains supporting information for the parameterization of cholesterol for the Martini 3 coarse grained force field. You can find here intermediary development cholesterol parameters, as well as the final Martini 3 cholesterol model. An insane.py script containing the new Martini 3 cholesterol model is also supplied. Alternatively, you can add the following entry to your own insane.py:

# Sterols
moltype = "sterol"
lipidsx[moltype] = (      0,   1,   0,   0,  1,   0, 0.5, 0.5,   0,  0)
lipidsy[moltype] = (      0,   0,   0,   0,  0,   0,   0,   0,   0,  0)
lipidsz[moltype] = (    5.3, 4.5, 3.9, 3.3,  3, 2.6, 4.5, 2.6, 1.4,  0)
lipidsa.update({
    "CHOL": (moltype, " ROH  R1  R2  R3  R4   -  R5  R6  C1  C2 "),
})

Footnotes

1. Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal; ↩ ↩² ↩³

2. Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS & University of Lyon, 7 Passage du Vercors, Lyon F-69367, France; ↩ ↩²

3. Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA; ↩ ↩² ↩³

4. Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Alberta, Canada; ↩ ↩²

5. Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany; ↩ ↩²

6. Frankfurt Institute for Advanced Studies, Ruth-Moufang-Straße 1, 60438 Frankfurt am Main, Germany: ↩

7. Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK; ↩

8. CiTIUS Intelligent Technologies Research Centre, University of Santiago de Compostela, Santiago de Compostela, Spain. ↩

9. Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands ↩