Slipids/AMBER Gromacs by XYZ

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Lipid 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC)
Pubchem CID:512874
Forcefield Slipids/AMBER
Code Gromacs
Authors Jämbeck JP, Lyubartsev AP
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Joakim Jämbeck

An all-atomistic force field (FF) for saturated PC lipids coined Stockholm lipids (Slipids). All parameters have been developed in a consistent and physical sound way. All the partial atomic charges have been recalculated at the B3LYP/cc-pVTZ level of theory by fitting the electrostatic potential. Lennard-Jones and torsional parameters were refitted from experimental data and high level ab-initio calculations, respectively. The remaining parameters are taken from C36.

The abilities of Slipids is proven in J. Phys. Chem. B, 2012, 116 (10), 3164-3179 (http://pubs.acs.org/doi/abs/10.1021/jp212503e, open access) and J. Chem. Theory Comput., 2012, DOI: 10.1021/ct300342n. A number of experimental properties such as area per lipid and thicknesses are reproduced. More importantly, X-ray and neutron scattering form factors and NMR order parameters are in excellent agreement with experiments for a range of temperatures.

Slipids is compatible with FFs from the AMBER family for amino acids. Tests with AMBER99SB, AMBER99SB-ILDN and AMBER03 together with Slipids have been performed with microsecond simulations and show that they can be mixed. Free energies of transfer of amino acid analogues from water to cyclohexane has also been calculated and are in good agreement with experimental data.

See http://people.su.se/~jjm for more parameters and related data such as structures etc.


Jämbeck JP, Lyubartsev AP, Derivation and systematic validation of a refined all-atom force field for phosphatidylcholine lipids., J Phys Chem B 116 (2012), 3164-79, doi: 10.1021/jp212503e, pubmed:22352995 [pubmed] [hubmed]
Primary Experimental

Jämbeck, J. P. M. and Lyubartsev, A. P., An Extension and Further Validation of an All-Atomistic Force Field for Biological Membranes, J. Chem. Theory Comput. (2012), doi: 10.1021/ct300342n, [no pubmed id]
Primary Experimental

Jämbeck, J. P. M. and Lyubartsev, A. P., Another Piece of the Membrane Puzzle: Extending Slipids Further, J. Chem. Theory Comput. (2012), doi: 10.1021/ct300777p, [no pubmed id]
Primary Experimental


Version 2
forcefield.ff.zip 7a30a7aaa40b5dca0070efad5ad847c95d662b26
PDB structure
Bilayer structure
Version 1
DLPC.itp 94e95e81c5034e630f9f91031bf580c15a2fce81
WebCite:http://web.me.com/jambeck/lipids/Downloads_files/DLPC.itp WebCiteID:
forcefield.ff.zip d3726c8636c7a86414f40c8f020799cd7c54df17
WebCite:http://web.me.com/jambeck/lipids/Downloads_files/forcefield.ff.zip WebCiteID:
PDB structure
Bilayer structure
DLPC_303K.gro 17e2434c15b069b6f200fabc1f03e8218c6879c2
DLPC_303K.pdb dd8ee0402e7a5074f6d14ee07a001fbddcfbfc04
DLPC_323K.gro 5cc932170b8205fd694028859d7ac7f23f66978f
DLPC_323K.pdb 60bcd2a27b3fd3e601cc0dd0fe8ebad25264a078
DLPC_333K.gro 1b82c70f11c2c11b102f9943cdabf425f6b50bf3