ProtoMS3.3 tutorials

The tutorials available for ProtoMS can be found below. For more information, please check the ProtoMS manual or documentation (provided with the download of ProtoMS).

  • Basic Monte Carlo sampling with ProtoMS, exploring the equilibration of the protein MUP-I complexed with a ligand
  • Relative solvation free energy of ethane and methanol
  • Absolute solvation free energy of 2-chlorosyringaldehyde
  • Relative binding free energy of ligands to COX2
  • Absolute binding free energy of benzene to T4 lysozyme
  • JAWS method for water placement in N-terminal domain of HSP90
  • Estimating the binding affinity of water with JAWS in HPS90
  • Estimating the decoupling free of a water molecule with GCMC in BPTI
  • GCMC titration and grand canonical integration
  • In all tutorials it is assumed that $PROTOMSHOME is set to the installation path of ProtoMS

    A visualization software is required in most tutorials to asses results of simulations as well as certain stages of set-up. Throughout the tutorials, VMD is recommemded. Nevertheless, please feel free to use the software of your choice.

    Current version of ProtoMS 3.3