Name

monte carlo free energy perturbation

Software

MCPro

Parameter

OPLS force field
RESP charges, at HF6-31G* level.
Windows per transformation: 20
Assumed pH 7.4
Typical simulation time per window: 50 ns
Monte Carlo thermostat with time constant of 2 ps
(etc.)

Method

The ligands were represented by the OPLS-AA force field and the TIP4P water model was used.
Metropolis Monte Carlo statistical mechanics (MC)
calculations were performed for a single solute in a periodic cube with 500 water molecules at
25 C and 1 atm in the isothermal-isobaric ensemble using MCPro.

Name

Glide xp

Software

Schrodinger2015

System Preparation Parameters

Assumed pH 7.4

System Preparation Method

Maestro's prepwizard was used to add hydrogens using default parameters.

Pose Prediction Parameters

Iterated Local Search global optimizer search method
Exhaustiveness=50 #exhaustiveness of global search (default=8)
Glide scoring funtion (empirical + knowledge-based function)
Num_modes=5 #max number of poses to generate
Energy_range=5 #energy difference (kcal/mol) between the best and worst binding mode

Pose Prediction Method

Docking runs were executed with the above specified parameters while default values
were applied for the rest of the variables. The top 5 poses from the Vina docking are submitted with this protocol.