Molecular dynamics simulations PksD AH

Restricted access for the review purposes. The data set will become open access upon paper acceptance.

Content of the zipped directories:

-> Non-standard_force_fields
This directory contains the parameters used for acetyl Ppant, malonyl Ppant and O-acetylserine in AMBER simulations.
    -> SAC.frcmod, SAC.mol2 - parameters for O-acetylserine.
    -> ACL.frcmod, ACL.mol2 - parameteres for acetyl phosphopantetheine
    -> MAL.frcmod, MAL.mol2 - parameters for malonyl phosphopantetheine
    
-> PksD_AH_Oas99
This directory contains AMBER MD trajectories and topology files for simulations involving PksD AH with O-acetylserine in position 99.
    -> stripped_topology_cMD.prmtop - topology file for the trajectory-cMD-initial.nc
    -> trajectory-cMD-initial.nc - initial 50 ns classical MD trajectory in AMBER NetCDF format. Sampled every 40 ps.
    -> closest_topology-aMD.prmtop - topology file for the trajectory trajectory-closest-aMD.nc. Only 3 closest water molecules retained.
    -> trajectory-closest-aMD.nc - ~320 ns accelerated MD trajectory in AMBER NetCDF format. Only 3 closest water molecules retained.
    -> closest_topology-cMD-f1650.prmtop - topology file for the trajectory trajectory-closest-cMD-final-f1650.nc. Only 3 closest water molecules retained.
    -> trajectory-closest-cMD-final-f1650.nc - 10 ns classical MD trajectory restarted from frame 1650 of the aMD. Only 3 closest water molecules retained.
    -> filtered_topology.prmtop - topology file for frames filtered by Bürgi-Dunitz criteria (here: His201[Nε2]-WAT[H] distance ≤ 3 Å, WAT[O]-Ac[C’] distance ≤ 3.2 Å and WAT[O]-Ac[C’]-Ac[O] angle 100°-110°).
    -> filtered_f1650_2323_H1.nc - trajectory fulfilling Bürgi-Dunitz criteria for H1 of water 2323
    -> filtered_f1650_2323_H2.nc - trajectory fulfilling Bürgi-Dunitz criteria for H2 of water 2323
    -> filtered_f1650_6673_H1.nc - trajectory fulfilling Bürgi-Dunitz criteria for H1 of water 6673
    -> filtered_f1650_6673_H2.nc - trajectory fulfilling Bürgi-Dunitz criteria for H2 of water 6673
    -> filtered_f1650_12895_H1.nc - trajectory fulfilling Bürgi-Dunitz criteria for H1 of water 12895
    -> filtered_f1650_12895_H2.nc - trajectory fulfilling Bürgi-Dunitz criteria for H2 of water 12895

-> PksD_AH_PksJ_ACP4_ACL
This directory contains AMBER MD trajectories and topology files for simulations involving PksD AH:PksJ ACP4 with acetyl Ppant. Both topology and trajectories are stripped of water and ions.
    -> stripped_topology.prmtop - topology file for the system
    -> trajectory-cMD-initial.nc - initial 50 ns classical MD trajectory in AMBER NetCDF format. Sampled every 20 ps.
    -> trajectory-aMD.nc - ~288 ns accelerated MD trajectory in AMBER NetCDF format. Sampled every 20 ps. Additional frames to 572 ns not included.
    -> trajectory-cMD-final-f3221.nc - 20 ns classical MD trajectory restarted from frame 3221 of the aMD. Sampled every 2 ps.
    -> trajectory-cMD-final-f4230.nc - 20 ns classical MD trajectory restarted from frame 4230 of the aMD. Sampled every 2 ps.
    -> filtered_trajectory-cMD-final-f3221.nc - trajectory-cMD-final-f3221.nc filtered for frames satisfying Bürgi-Dunitz conditions(here: His201[Nε2]-Ser99[H] distance ≤ 3 Å, Ser99[OG]-Ac[C’] distance ≤ 3.2 Å and Ser[OG]-Ac[C’]-Ac[O] angle 100°-110°).
    -> filtered_trajectory-cMD-final-f4230.nc - trajectory-cMD-final-f4230.nc filtered for frames satisfying Bürgi-Dunitz conditions(here: His201[Nε2]-Ser99[H] distance ≤ 3 Å, Ser99[OG]-Ac[C’] distance ≤ 3.2 Å and Ser[OG]-Ac[C’]-Ac[O] angle 100°-110°).

-> PksD_AH_PksJ_ACP4_MAL
This directory contains AMBER MD trajectories and topology files for simulations involving PksD AH:PksJ ACP4 with malonyl Ppant. Both topology and trajectories are stripped of water and ions.
    -> stripped_topology.prmtop - topology file for the system
    -> trajectory-cMD-initial.nc - initial 50 ns classical MD trajectory in AMBER NetCDF format
    -> trajectory-aMD.nc - ~281 ns accelerated MD trajectory in AMBER NetCDF format. Sampled every 20 ps.
    -> trajectory-cMD-final.nc - 50 ns classical MD trajectory restarted from frame 8549 of the aMD. Sampled every 5 ps.