Slipids Force Field v2.0 (2016)

DOI10.5281/zenodo.1149623Zenodo1149623MaRDI QIDQ6701703

Dataset published at Zenodo repository.

Author name not available (Why is that?)

Publication date: 16 January 2018

Copyright license: No records found.

Description

Slipids force field: files for Gromacs ----------------------------------------------------------- Authors: Joakim Jmbeck, Inna Ermilova, Alexander Lyubartsev Department of Materials and Environmental Chemistry, Stockholm University, Stockholm 10691 Sweden e-mail: alexander.lyubartsev@mmk.su.se Content: SLipids_FF: directory containing the force field. Included into the Gromacs topology file by: #include SLipids_FF/forcefield.itp itp_files: itp files for various lipids The force field can be used together with the AMBER99SB/AMBER03/GAFF for proteins  !!!! MAKE SURE YOU CITE THE FOLLOWING REFERENCES WHEN USING THIS FORCE FIELD ! Saturated PC lipids: Joakim P. M. Jmbeck and Alexander P. Lyubertsev, Derivation and Systematic Validation of a Refined All-Atom Force Field for Phosphatidylcholine Lipids, J. Phys. Chem. B, 2012, 116, 3164-3179 (2012) DOI: 10.1021/jp212503e POPC, DOPC, SOPC, DOPE, POPE and similar: Joakim P. M. Jmbeck and Alexander P. Lyubertsev, An Extension and Further Validation of an All-Atomistic Force Field for Biological Membranes J. Chem. Theory Comput., 8, 2938-2948, (2012) DOI: 10.1021/ct300342n PS, PG, SM lipids and Cholesterol: Joakim P. M. Jmbeck and Alexander P. Lyubertsev, Another Piece of the Membrane Puzzle: Extending Slipids Further J. Chem. Theory Comput., 9 (1), 774-784 (2013) DOI: 10.1021/ct300777p Polyinsaturated lipids: Inna Ermilova and Alexander Lyubartsev:, Extension of the Slipids Force Field for Polyunsaturated Lipids, J. Phys. Chem. B, 120 (50), 1282612842 (2016) Cite also this paper on Charmm36 force field since bond and angle parameters, as well as a part of Lennard-Jones parameters and torsion angles in the lipid headgroups in SLipids are taken from the Charmm36 force field: Jeffery B. Klauda, Richard M. Venable, Alfredo Freites, Joseph W. OConnor, Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor Vorobyov, Alexander D. MacKerell, Jr. and Richard W. Pastor, Update of the CHARMM all-atom additive force field for lipids: Validation on six lipid types, J.Phys.Chem B, 114, 783078 (2010)

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