Strucutral basis of drug efflux by the staphylococcal multidrug efflux pump QacA

This repository contains files to replicate Molecular Dynamics simulations of the QacA multidrug efflux pump.

These files are associated with the following publication:

Citation Pending

Contents:

.
|___README.md # This file
|
|___prod.mdp # Molecular Dynamics production run parameters
|
|___gromos54a7_atb.ff # Contains the GROMOS 54a7 force field files and the ATB parameters for the ligands used in these simulations
|
|___input
    |___Outward
    |   |___Apo
    |   |   |___QacA_outward_apo_HE406-407_ecoli_r1_start.gro
    |   |   |___QacA_outward_apo_HE406-407_ecoli_r1.top
    |   |   |___QacA_outward_apo_HE406-407_ecoli_r1.ndx
    |   |   |___QacA_outward_apo_HE406-407_ecoli_r1.tpr
    |   |   |___QacA_outward_apo_HE406-407_ecoli_r2_start.gro
    |   |   |___QacA_outward_apo_HE406-407_ecoli_r2.top
    |   |   |___QacA_outward_apo_HE406-407_ecoli_r2.ndx
    |   |   |___QacA_outward_apo_HE406-407_ecoli_r2.tpr
    |   |   |___QacA_outward_apo_HE406-407_ecoli_r3_start.gro
    |   |   |___QacA_outward_apo_HE406-407_ecoli_r3.top
    |   |   |___QacA_outward_apo_HE406-407_ecoli_r3.ndx
    |   |   |___QacA_outward_apo_HE406-407_ecoli_r3.tpr
    |   |   
    |   |___Ethidium
    |       |___E407
    |       |   |___QacA_outward_etbr_E407_ecoli_r1_start.gro
    |       |   |___QacA_outward_etbr_E407_ecoli_r1.top
    |       |   |___QacA_outward_etbr_E407_ecoli_r1.ndx
    |       |   |___QacA_outward_etbr_E407_ecoli_r1.tpr
    |       |   |___QacA_outward_etbr_E407_ecoli_r2_start.gro
    |       |   |___QacA_outward_etbr_E407_ecoli_r2.top
    |       |   |___QacA_outward_etbr_E407_ecoli_r2.ndx
    |       |   |___QacA_outward_etbr_E407_ecoli_r2.tpr
    |       |   |___QacA_outward_etbr_E407_ecoli_r3_start.gro
    |       |   |___QacA_outward_etbr_E407_ecoli_r3.top
    |       |   |___QacA_outward_etbr_E407_ecoli_r3.ndx
    |       |   |___QacA_outward_etbr_E407_ecoli_r3.tpr
    |       |___HE407
    |       |   |___QacA_outward_etbr_HE407_ecoli_r1_start.gro
    |       |   |___QacA_outward_etbr_HE407_ecoli_r1.top
    |       |   |___QacA_outward_etbr_HE407_ecoli_r1.ndx
    |       |   |___QacA_outward_etbr_HE407_ecoli_r1.tpr
    |       |   |___QacA_outward_etbr_HE407_ecoli_r2_start.gro
    |       |   |___QacA_outward_etbr_HE407_ecoli_r2.top
    |       |   |___QacA_outward_etbr_HE407_ecoli_r2.ndx
    |       |   |___QacA_outward_etbr_HE407_ecoli_r2.tpr
    |       |   |___QacA_outward_etbr_HE407_ecoli_r3_start.gro
    |       |   |___QacA_outward_etbr_HE407_ecoli_r3.top
    |       |   |___QacA_outward_etbr_HE407_ecoli_r3.ndx
    |       |   |___QacA_outward_etbr_HE407_ecoli_r3.tpr
    |
    |___Inward
       |___Apo
       |   |___QacA_inward_apo_HD411_ecoli_r1_start.gro
       |   |___QacA_inward_apo_HD411_ecoli_r1.top
       |   |___QacA_inward_apo_HD411_ecoli_r1.ndx
       |   |___QacA_inward_apo_HD411_ecoli_r1.tpr
       |   |___QacA_inward_apo_HD411_ecoli_r2_start.gro
       |   |___QacA_inward_apo_HD411_ecoli_r2.top
       |   |___QacA_inward_apo_HD411_ecoli_r2.ndx
       |   |___QacA_inward_apo_HD411_ecoli_r2.tpr
       |   |___QacA_inward_apo_HD411_ecoli_r3_start.gro
       |   |___QacA_inward_apo_HD411_ecoli_r3.top
       |   |___QacA_inward_apo_HD411_ecoli_r3.ndx
       |   |___QacA_inward_apo_HD411_ecoli_r3.tpr
       |___Ethidium
           |___QacA_inward_etbr_HD411_ecoli_r1_start.gro
           |___QacA_inward_etbr_HD411_ecoli_r1.top
           |___QacA_inward_etbr_HD411_ecoli_r1.ndx
           |___QacA_inward_etbr_HD411_ecoli_r1.tpr
           |___QacA_inward_etbr_HD411_ecoli_r2_start.gro
           |___QacA_inward_etbr_HD411_ecoli_r2.top
           |___QacA_inward_etbr_HD411_ecoli_r2.ndx
           |___QacA_inward_etbr_HD411_ecoli_r2.tpr
           |___QacA_inward_etbr_HD411_ecoli_r3_start.gro
           |___QacA_inward_etbr_HD411_ecoli_r3.top
           |___QacA_inward_etbr_HD411_ecoli_r3.ndx
           |___QacA_inward_etbr_HD411_ecoli_r3.tpr