MD simulations of P-glycoprotein started from three different crystal strucures: 3G5U, 4M1M and 4KSB

Molecular simulations of mouse P-glycoprotein started from three different crystal structures with PDB IDs corresponding to 3G5U, 4KSB and 4M1M. The protein was transferred to POPC/cholesterol bilayer, followed by energy minimization and 10 ns equilibration period. All the simulations were performed in Gromacs 3.3.3 in conjunction with GROMOS54a7 force field at 300 K and pressure of 1 bar. Each system was run in triplicates for 200 ns. <br><br>The uploaded fileset contains:<br> - MD protocol used to run simulations for 3G5U, 4M1M and 4KSB systems; <br><br> - Example input file for a production run for each system (3G5U_run1.mdp, 4M1M_run1.mdp, 4KSB_run1.mdp);<br><br> - System topologies (3G5U_memb.top, 4M1M_memb.top, 4KSB_memb.top) and relevant parameter files (3g5u.itp, 4m1m.itp, 4ksb.itp, CLR.itp, POPC.itp, vdw_OML_CH3L.itp); <br> <br> - Set of three trajectories containing membrane-embedded P-glycoprotein with 1000 frames for each simulated system (snapshots printed every 200 ps);<br><br> - Movies generated from each trajectory with a more detailed description provided in <i>Movie_Legends.pdf</i>. <br><br><br>