Slipids force field: files for Gromacs ----------------------------------------------------------- Authors: Joakim Jämbeck, 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. Jämbeck 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. Jämbeck 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. Jämbeck 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), 12826–12842 (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. O’Connor, 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, 7830–78 (2010)

{"references": ["Joakim P. M. J\u00e4mbeck 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", "Joakim P. M. J\u00e4mbeck 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", "Joakim P. M. J\u00e4mbeck 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", "Inna Ermilova and Alexander Lyubartsev:, \"Extension of the Slipids Force Field for Polyunsaturated Lipids\", J. Phys. Chem. B, 120 (50), 12826\u201312842 (2016)"]}

Funding: Swedish Research Council (Vetenskapsrådet)