ProtoMS3.0 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 decoupling free of a water molecule with GCMC in BPTI
In all tutorials it is assumed that $PROTOMSHOME
is set to the installation path of ProtoMS3.0