Slipids Force Field V2.0 (2016)
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Slipids force field: files for Gromacs<br> ----------------------------------------------------------- Authors: Joakim Jämbeck, Inna Ermilova, Alexander Lyubartsev<br> Department of Materials and Environmental Chemistry,<br> Stockholm University, Stockholm 10691 Sweden<br> e-mail: alexander.lyubartsev@mmk.su.se Content: SLipids_FF: directory containing the force field. Included into the Gromacs<br> topology file by: <br> #include "SLipids_FF/forcefield.itp" itp_files: itp files for various lipids The force field can be used together with the AMBER99SB/AMBER03/GAFF<br> for proteins <br> !!!! MAKE SURE YOU CITE THE FOLLOWING REFERENCES WHEN USING THIS FORCE FIELD ! <br> Saturated PC lipids: Joakim P. M. Jämbeck and Alexander P. Lyubertsev, "Derivation and Systematic<br> Validation of a Refined All-Atom Force Field for Phosphatidylcholine Lipids",<br> J. Phys. Chem. B, 2012, 116, 3164-3179 (2012) DOI: 10.1021/jp212503e POPC, DOPC, SOPC, DOPE, POPE and similar:<br> <br> Joakim P. M. Jämbeck and Alexander P. Lyubertsev, "An Extension and Further<br> Validation of an All-Atomistic Force Field for Biological Membranes"<br> 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<br> Membrane Puzzle: Extending Slipids Further"<br> 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<br> Field for Polyunsaturated Lipids",<br> J. Phys. Chem. B, 120 (50), 12826–12842 (2016) <br> Cite also this paper on Charmm36 force field since bond and angle parameters,<br> as well as a part of Lennard-Jones parameters and torsion angles in the lipid<br> headgroups in SLipids are taken from the Charmm36 force field: Jeffery B. Klauda, Richard M. Venable, Alfredo Freites, Joseph W. O’Connor,<br> Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor Vorobyov, Alexander D.<br> MacKerell, Jr. and Richard W. Pastor, "Update of the CHARMM all-atom additive<br> force field for lipids: Validation on six lipid types", J.Phys.Chem B, 114,<br> 7830–78 (2010)
