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

Slipids/AMBER Gromacs by XYZ

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Lipid 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC)
Pubchem CID:5364680
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 2
Topology
DOPC.itp c088f0204b4bb50098da748bdf88554f86d487b6
Parameters
forcefield.ff.zip 7bace907f100c30d9bcbd1238ddf3c29742b0e49
PDB structure
Bilayer structure
Version 1
Topology
DOPC.itp c088f0204b4bb50098da748bdf88554f86d487b6
Parameters
forcefield.ff.zip 472f61e116bf906d6db10914e61fac037c832632
PDB structure
Bilayer structure
DOPC_323K.gro 0708ea5191e2620e6cbc7e793cfd565400c7c58b
DOPC_293K.gro 6acb7ca93bdefa4cb38304c5a9b70e173f004221
DOPC_333K.gro 1aa81296607e46413b99f12a6b5c4116865f6095
DOPC_303K.gro 593e00b8986e08bcedc6570700ab63ab1bab6926