Idea of the project: comparison of the behavior of three different variants of b2m (the same we're studying in Proline Metadynamics),that are D76N (the most amyloidogenical), W60G (the anti-aggregation) and WT, once they are interacting with graphite
Main steps: docking  -->  500ns classic MD  -->  parallel tempered Metadynamics
In the same experimental conditions used by Mangione, the three variant result protonated this way:
PQR file (containing charges and vdW radius) are requested as input for SDA 7.2 software

SDA 7.2 Simulation of Diffusional Association software

Main steps
  1. generate pqr files for each solute (with protonation states for the experimental conditions to be modeled)
  2. Compute Poisson-Boltzmann electrostatic potential grids
  3. Compute the effective charges (Effective Charges for Macromolecules)
  4. Compute the other grids: electrostatic desolvation, hydrophobic desolvation and soft-core repulsive grids
  5. Docking production simulations with default probes probep = 1.7 probew = 1.4 ( sum =3.1 Å represents an approximation to the length of a hydrogen bond)

Result of docking clusters

Wild Type

N      step  cl_ size  energy  cl_size with SDA
   1    177620   453    -6.479e+01  1.258137e+06    (intersection between LYS74 and 3layer)
   2     53766   749    -7.907e+01  2.379139e+06
   3    149515     5    -7.891e+01  2.476000e+04
   4     43704   168    -6.940e+01  4.494750e+05
   5    133836   134    -6.959e+01  4.293740e+05
   6     90677    15    -6.541e+01  1.554900e+04
   7     98819    18    -6.112e+01  1.312500e+04
   8     25355   449    -5.951e+01  9.609290e+05
## RunNb      StepNb      TotEn                         El                    ED                        HD                        rLJ           Occur          AvEnergy       StdAvEnergy
      54      177620         -1.1079E+02      0.0000E+00      2.9168E+01     -1.1734E+01     -1.2823E+02    453        -6.479e+01       1.258137e+06
      25       53766           -8.4132E+01     0.0000E+00      9.3869E+00     -7.9987E+00     -8.5520E+01     749       -7.907e+01       2.379139e+06
      28      149515        -7.9696E+01      0.0000E+00      1.8096E+01     -1.0105E+01     -8.7687E+01       5          -7.891e+01       2 .476000e+04
      20       43704          -7.2527E+01      0.0000E+00      7.7342E+00     -6.4271E+00     -7.3834E+01    168        -6.940e+01       4.494750e+05
      83      133836        -7.1902E+01      0.0000E+00      9.8352E+00     -6.9440E+00     -7.4793E+01     134        -6.959e+01       4.293740e+05
      34       90677         -6.5922E+01      0.0000E+00      9.0404E+00     -6.0320E+00     -6.8931E+01      15          -6.541e+01       1.554900e+04
      77       98819          -6.3945E+01     0.0000E+00      2.1447E+01     -7.9523E+00     -7.7440E+01       18        -6.112e+01       1.312500e+04
      38       25355          -6.0649E+01     0.0000E+00      8.7353E+00     -6.3685E+00     -6.3016E+01       449        -5.951e+01       9.609290e+05