6 most abundant equilibrated milk proteins

This dataset contains the equilibrated PDBs for six most abundant milk proteins, namely αs1-casein, αs2-casein, β-casein, α-lactalbumin, β-lactoglobulin and Bovine Serum Albumin using Molecular Dynamics. The 3D structure of the proteins has been created by Dr. Julia Subbotina using ITASSER from the AA sequences. Then I performed GROMACS for energy minimisation and equilibration. The system was solvated using the original form of TIP3 water model and It was then neutralized by NaCl regarding the charge of the whole system. In the MD calculation the energy of the system has been minimized by Verlet particle-based cut-off scheme using charge groups and steepest gradient method for 10000 steps. The system was equilibrated under constant pressure, particles and temperature (300 K) condition (NPT) using Berendsen weak coupling for 10.0 ns. The component of the pressure tensor were set to 1.0 bar. The thermostat and the barostat for the relaxation time was 1.0 ps. The system underwent another more unbiased equilibrations for 20 ns in the NVT ensemble conditions. The Nose-Hoover thermostat's relaxation time constant for the NVT ensemble was 5 ps. The cut-off distance was set to 1.0 nm for the VdW short range interactions. After analysing the RMSD (Root Mean Square Deviation) as a function of time, the