1,2-dipalmitoyl-sn-glycero-3-phosphocholine

Slipids/AMBER Gromacs by XYZ

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Lipid 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC)
Pubchem CID:6139
Forcefield Slipids/AMBER
Code Gromacs
Authors Jämbeck JP, Lyubartsev AP
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Joakim Jämbeck
Abstract



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.



References

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

Versions

Version 3
Topology
Parameters
forcefield.ff.zip 7a30a7aaa40b5dca0070efad5ad847c95d662b26
PDB structure
Bilayer structure
Version 2
Topology
Parameters
forcefield.ff.zip 472f61e116bf906d6db10914e61fac037c832632
PDB structure
Bilayer structure
Version 1
Topology
DPPC.itp 2a97ede21ebc7773649efbca32d969b43fbc5f57
WebCite:http://web.me.com/jambeck/lipids/Downloads_files/DPPC.itp WebCiteID: 67M7YfTla
Parameters
forcefield.ff.zip d3726c8636c7a86414f40c8f020799cd7c54df17
WebCite:http://web.me.com/jambeck/lipids/Downloads_files/forcefield.ff.zip WebCiteID: 67M7YkCTA
PDB structure
Bilayer structure
DPPC_293K.gro 5e2a1d830807132ebaf6580c7cbbad3f1f7ffdc5
DPPC_323K.gro a19a0b576953cf213850f2015b45a8800244c342
DPPC_333K.gro ea8a1546f0f4684d7035d87c0ee36aaba22df559
DPPC_353K.gro 2d935264e2ea7f9c45b8c270b1957917afaf1707