RSS Most recent package AMBER-GAFF Amber 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine by cd709

Viewing lipid POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine)

Name 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine
Shorthand POPE
Pubchem 5282290
CAS RN 26662-94-2

Associated packages

CHARMM36 Gromacs
POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine)

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Lipid POPE 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine
Forcefield CHARMM36
Code Gromacs
Authors Klauda, Jeffery B and Venable, Richard M and Freites, J Alfredo and O'Connor, Joseph W and Tobias, Douglas J and Mondragon-Ramirez, Carlos and Vorobyov, Igor and MacKerell, Jr, Alexander D and Pastor, Richard W
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Creation date 06 Mar 2012

156 POPE lipids equilibrated for 40 ns

surface per lipid 0.572 nm^2

 

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GROMOS-CKP Gromacs
POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine)

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Lipid POPE 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine
Forcefield GROMOS-CKP
Code Gromacs
Authors Piggot TJ, Holdbrook DA, Khalid S
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Creation date 22 May 2012

POPE GROMOS-CKP lipid parameters. These lipid parameters can be used with the GROMOS 53A6 and GROMOS 54A7 protein force fields without any modifications to the parameters.

If you use these parameters please read and cite:

Electroporation of the E. coli and S. aureus Membranes: Molecular Dynamics Simulations of Complex [...] [read more]

GROMOS43A1-S3 Gromacs
POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine)

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Lipid POPE 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine
Forcefield GROMOS43A1-S3
Code Gromacs
Authors Chiu SW, Pandit SA, Scott HL, Jakobsson E
Licence fair use
Creation date 01 Jun 2012

A new GROMOS43a1-based force field (43A1-S3) for simulation of membranes with the  Gromacs simulation package. The validity of the force fields is demonstrated by correct replication of X-ray form factors and NMR order parameters over a wide range of membrane compositions in semi-isotropic NTP [...] [read more]

Slipids/AMBER Gromacs
POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine)

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Lipid POPE 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine
Forcefield Slipids/AMBER
Code Gromacs
Authors Jämbeck JP, Lyubartsev AP
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Creation date 14 Jul 2012

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 [...] [read more]

AMBER-GAFF Amber
POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine)

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Lipid POPE 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine
Forcefield AMBER-GAFF
Code Amber
Authors -
Licence Public Domain Open Knowledge
Creation date 09 Oct 2013

GAFFlipid parameter files for simulation of POPE using AMBER. Also included are PDB files of 72, 288 and 2x288 POPE bilayers.

 

To unzip: tar -xvzf POPE.tgz

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