Name

MMPBSA_WSAS (PBSA_DELPHI)

Software

Amber16

Parameters

Assumed pH 7.4
Typical simulation time per complex system: 5 ns
10 structures were taken from every ns of the MD simulation for the mmpbsa_wsas calculation

Method

The initial structure of the complex system corresponding to each ligand was taken from the best docking pose.
The structure was then placed in a octagonal box with 7300 TIP3P water molecule. The solvet system went through following steps:
minimization with constrain all atoms of the ligand and protein, minimization without any constrain, heat up to 310 K, run equilibrium 1 ns with constrain all protein atoms
and following by 5 ns with constrain the protein backbone. The srtuctures taken form the last 5 ns for every 100 ps were used for mmpbsa_wsas calculation.

Answer 1

No

Name

Openbabel/Amber16/MGLTools/Autodock Vina

Software

Openbabel/Amber16/MGLTools/Autodock Vina Method 1

System Preparation Parameters

Assumed pH 7.4
Tautomers considered
AM1-BCC charges

System Preparation Method

Openbabel was used for generating 3D structures in pdb format of the ligands from their smile format.
The mol2 of the generated 3D ligands then were created by using antechamber with the net charges taken from the smile format applying AM1-BCC1 method.
Thi pdbqt format of the ligands which will be used as input for ligands in Autodock Vina docking were prepared by MGLTools from their mol2 format and keeping their charge information.
The protein was added missing Hydrogen and side chain atoms by using Ambertools. The input file of the receptor for the docking was prepared by MGLTools.
The GAFF force field parameters were assigned to all the ligands, while the amber99SBildn force field was applied for the protein.
In this docking, the docking rectangle box was chosen to covered all the receptor with the minimum distance between protein and box's walls is 7 angstrong.

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

No