Conformational Plasticity of β-rich Proteins: Molecular Insights into Stability, Dynamics, and Functional Adaptation of Bet v 1-like Proteins (Q6703004)

The zip files contain data related to individual molecular dynamics simulations. The contents of each archive are as follows:*archive*.pdb - Initial Structure*archive*_solv.pdb - Start Structure (Solvated)*archive*.prmtop - Initial Topology *archive*.inpcrd - Initial Velocities*archive*.mdcrd - Representative Trajectory File Min.in - Input for First Minimization Min-II.in - Input for Seccond Minimization stage1_heat_5_50K_for_10ps.in - Input for Heating from 5K to 50K in 10 psstage1.rst - Restart Heating from 5K to 50K in 10 psstage1.out - Log for Heating from 5K to 50K in 10 psstage1.mdcrd - Trajectory of Heating from 5K to 50K in 10 ps stage1_equil_50K_for_100ps.in - Equilibration in 50K for 100 psstage2.rst - Restart Equilibration in 50K for 100 psstage2.out - Log for Equilibration in 50K for 100 psstage2.mdcrd - Trajectory of Equilibration in 50K for 100 ps stage2_heat_50_100K_for_10ps.in - Input for Heating from 50K to 100K in 10 psstage3.rst - Restart Heating from 50K to 100K in 10 psstage3.out - Log for Heating from 50K to 100K in 10 psstage3.mdcrd - Trajectory of Heating from 50K to 100K in 10 ps stage2_equil_100K_for_100ps.in - Input for Equilibration in 100K for 100 psstage4.rst - Restart Equilibration in 100K for 100 psstage4.out - Log for Equilibration in 100K for 100 psstage4.mdcrd - Trajectory of Equilibration in 100K for 100 ps stage3_heat_100_150K_for_10ps.in - Input for Heating from 100K to 150K in 10 psstage5.rst - Restart Heating from 50K to 100K in 10 psstage5.out - Log for Heating from 50K to 100K in 10 psstage5.mdcrd - Trajectory of Heating from 50K to 100K in 10 ps stage3_equil_150K_for_100ps.in - Input for Equilibration in 150K for 100 psstage6.rst - Restart Equilibration in 150K for 100 psstage6.out - Log for Equilibration in 150K for 100 psstage6.mdcrd - Trajectory of Equilibration in 150K for 100 ps stage4_heat_150_200K_for_10ps.in - Input for Heating from 150K to 200K in 10 psstage7.rst - Restart Heating from 150K to 200K in 10 psstage7.out - Log for Heating from 150K to 200K in 10 psstage7.mdcrd - Trajectory of Heating from 150K to 200K in 10 ps stage4_equil_200K_for_100ps.in - Input for Equilibration in 200K for 100 psstage8.rst - Restart Equilibration in 200K for 100 psstage8.out - Log for Equilibration in 200K for 100 psstage8.mdcrd - Trajectory of Equilibration in 200K for 100 ps stage5_heat_200_250K_for_10ps.in - Input for Heating from 200K to 250K in 10 psstage9.rst - Restart Heating from 200K to 250K in 10 psstage9.out - Log for Heating from 200K to 250K in 10 psstage9.mdcrd - Trajectory of Heating from 200K to 250K in 10 ps stage5_equil_250K_for_100ps.in - Input for Equilibration in 250K for 100 psstage10.rst - Restart Equilibration in 250K for 100 psstage10.out - Log for Equilibration in 250K for 100 psstage10.mdcrd - Trajectory of Equilibration in 250K for 100 ps stage6_heat_250_300K_for_10ps.in - Input for Heating from 250K to 300K in 10 psstage11.rst - Restart Heating from 250K to 300K in 10 psstage11.out - Log for Heating from 250K to 300K in 10 psstage11.mdcrd - Trajectory of Heating from 250K to 300K in 10 ps stage6_equil_300K_for_5000ps.in - Input for Equilibration in 300K for 5000 psstage12.rst - Restart Equilibration in 300K for 5000 psstage12.out - Log for Equilibration in 300K for 5000 psstage12.mdcrd - Trajectory of Equilibration in 300K for 5000 ps Prod.in - Input for Step for Production (2 ns)