Name

MMPBSA (DELPHI) scaled

Software

AMBER16

Parameters

Assumed pH 5.0
Typical simulation time per MD: 50 ns

Method

The ligands were represented by the GAFF force field and the TIP3P water model was used.
Regular MD simulation of 5x10 ns and followed with our in-house version of MMPBSA calculation.
Each simulatin box includes one protein, one ligand, 13869 water molecules, ~ 38 Na+ and 38 Cl- ions.
The protonation states of ligands were set at pH 5.0.

Answer 1

No

Name

Amber16

Software

Amber16

System Preparation Parameters

Assumed pH 3:7
AM1-RESP charges

System Preparation Method

The GAFF force field parameters were assigned to all the ligands, while the amber ff14SB force field was applied for the protein.
AMBERTOOLS16 was used to generate the 3D structures and AMBER16 was used to do the regular MD simulations

Pose Prediction Parameters

Iterated Local Search global optimizer search method
Exhaustiveness=150 #exhaustiveness of global search (default=8)
Vina scoring funtion (empirical + knowledge-based function)
Num_modes=20 #max number of poses to generate
Energy_range=7 #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.

Answer 1

No

Answer 2

Yes