Materials used in simulating and analysing the simulations of P-glycoprotein in a POPC/CHOL bilayer in 5 different force fields: AMBER 99SB-ILDN, CHARMM 36, OPLS-AA/L, GROMOS 54A7, MARTINI 2.2
Materials are available in data/.
Analysis code used is available in analysis/.
The AMBER 99SB-ILDN force field was published in [1]. Lipid parameters were obtained from SLipids, at [2].
The CHARMM 36 force field was published in [3]. The lipid membrane was built with CHARMM-GUI ([4], [5]) using lipid parameters from [6].
The OPLS-AA/L force field was published in [7]. Lipid parameters were obtained from [8] and [9].
The GROMOS 54A7 force field was published in [10]. Lipid parameters were published in [11] and [12].
The MARTINI 2.2 force field was published in [13]. The bilayer was generated with insane [14].
Analysis was conducted with cpptraj [15] and Python code. The Python code was built on MDAnalysis [16][17] and MDTraj [18]. The seaborn [19] and Plotly [20] libraries were used in visualisation.
All material is provided under an MIT license. Please cite the above references if you use this material in published work.
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