EmrE MD Simulation Coordinates and Simulation Parameters

coordinates.zip :
Coordinates for EmrE complexes generated by molecular dynamics simulation.
Water, ions and lipid atoms are not included.
Authors : V.Ovchinnikov, T.Stone, C.Deber and M.Karplus, 2017.
Simulation Program : ACEMD (Harvey et al, JCTC, 2009)
Simulation Forcefield : CHARMM36 (protein, water, ions and lipid),
CGENFF v.2b8 initial parameters for TPP+ and ethidium+
(Vanommeslaeghe, JCC, 2009), optimized using FFTK
(Mayne et al., JCC, 2013).
Simulation parameters : time step 2fs, SHAKE, nonbonded cutoff 12A,
CHARMM switching function active at 10A, PME electrostatics with 4th
order splines, NVT ensemble using Langevin thermostat with 0.1/ps friction.
Protein immersed in TIP3 water model, and DMPC lipid.
Coordinates are taken from the end of MD simulation in intervals of 20ns.
For EmrE/stapled peptide complexes, only the last coordinate set is given.

parameters.zip:
CHARMM-compatible simulation (force-field) parameters for simulating stapled peptides,
tetraphenylphosphonium and ethidium cations.
generated using CHARMM General Force Field (CGenFF) program versions
0.9.6-7b. Charges optimized using FFTK ( C.G. Mayne, J. Saam, K.
Schulten, E. Tajkhorshid, J.C. Gumbart. J. Comput. Chem. 2013, DOI:
10.1002/jcc.23422.)
The CGENFF topology file must be loaded prior to using this file
Authors : V.Ovchinnikov, T.Stone, C.Deber and M.Karplus, 2017