D-erythro-n-palmitoyl-sphingomyelin

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Lipid	D-erythro-n-palmitoyl-sphingomyelin (SM) Pubchem CID:9939941
Forcefield	GROMOS87
Code	Gromacs
Authors	Niemelä PS, Ollila S, Hyvönen MT, Karttunen M, Vattulainen I
Licence
Curator	Jan Domanski
Abstract	Sphingomyelin atomistic parameters developed by Perttu Niemelä and Ilpo Vattulainen. For validation of the parameters, see: Niemelä P, Hyvönen MT, Vattulainen I (2004) Structure and dynamics of sphingomyelin bilayer: Insight gained through systematic comparison to phosphatidylcholine. Biophys J 87: 2976–2989. The lipid.itp comes from P. Tieleman's lab webpage. The ffgmx*.* are the gromos parameters (come with Gromacs package). Both of these files are the versions available in 2007.

References

Niemelä PS, Ollila S, Hyvönen MT, Karttunen M, Vattulainen I, Assessing the nature of lipid raft membranes., PLoS Comput Biol 3 (2007), e34, doi: 10.1371/journal.pcbi.0030034, pubmed:17319738 [pubmed] [hubmed]
Primary Experimental

Berger O, Edholm O, Jähnig F, Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature., Biophys J 72 (1997), 2002-13, doi: 10.1016/S0006-3495(97)78845-3, pubmed:9129804 [pubmed] [hubmed]
Primary Experimental

Niemelä P, Hyvönen MT, Vattulainen I, Structure and dynamics of sphingomyelin bilayer: insight gained through systematic comparison to phosphatidylcholine., Biophys J 87 (2004), 2976-89, doi: 10.1529/biophysj.104.048702, pubmed:15315947 [pubmed] [hubmed]
Primary Experimental

Versions

Version	2
Topology	WebCite:http://moose.bio.ucalgary.ca/files/lipid.itp WebCiteID: 64YIuVHSN sm160.itp 3b7e4638ef7653b117828c01f3f29fc173ac9a3d ffgmx.itp 02283f8f12fc90fe08260461db72fdb8244d6c7e ffgmxbon.itp 9679f35c389a6f4da9e2f0b6ff02a72ece6e97b9 ffgmxnb.itp 4fdcf8c4a7630bcd9abbd4629168ce12bead5d13
Parameters
PDB structure	sphingomyelin-single.gro 13e27fa6c2d484989fb24751c78b4c5b93f2f732
Bilayer structure
View discussion Download (.zip)

Version	1
Topology	sm160.itp 3b7e4638ef7653b117828c01f3f29fc173ac9a3d ffgmx.itp 02283f8f12fc90fe08260461db72fdb8244d6c7e ffgmxbon.itp 9679f35c389a6f4da9e2f0b6ff02a72ece6e97b9 ffgmxnb.itp 4fdcf8c4a7630bcd9abbd4629168ce12bead5d13 lipid.itp 43c6b5d9bdb0c35fef4e35bf6f08b1937559d866
Parameters
PDB structure	sphingomyelin-single.gro 13e27fa6c2d484989fb24751c78b4c5b93f2f732
Bilayer structure
View discussion Download (.zip)