ProtoMS3.4 tutorials

Although there are many overlapping concepts in the below tutorials, they are arranged in order of complexity of application. You might like to start at the beginning and work your way through. We also suggest using the materials of a past ProtoMS workshop as a guide - you should be able to find the latest event easily via our website

  • 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 binding free energy of a water molecule network with GCMC in BPTI
  • Estimating a relative binding free with a trapped water using Grand Canonical Alchemical Perturbation in Scytalone
  • A closer look at the free energy analysis tools avaliable in ProtoMS

    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 recommended. Nevertheless, please feel free to use the software of your choice.