EmrE MD Simulation Coordinates and Simulation Parameters

Published: 25 January 2018| Version 2 | DOI: 10.17632/3pvz4hytfd.2


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



Harvard University


Biophysics, Molecular Simulation, Computational Chemistry