bxxm2-FreeEnergyProtocol.txt

Name

AMBER/MMPBSA/ELIE

Software

Amber

Parameters

Assumed pH 5.0
Typical simulation time per MD: 10 ns

Method

The ligands were represented by the GAFF force field and the TIP3P water model was used.
Two protein structures were used as receptors: 3IEJ, GABJ. The protonation states of ligands were set at pH 5.0.
Regular MD simulation of 10 ns were performed and followed with our in-house version of MMPBSA calculation,
and then processed by Extended Linear Interaction Energy (ELIE) model.

Answer 1

No

bxxm2-PosePredictionProtocol.txt

Name

AMBER Method 1

Software

Amber

System Preparation Parameters

Assumed pH 5
Tautomers considered

System Preparation Method

Two protein structures were used as receptor: 3IEJ, GABJ.
All the waters were retained while GAFF force field parameters were assigned to the protein and all
ligands.

Pose Prediction Parameters

MD simulations

Pose Prediction Method

MD simulations with explicit water molecules.

Answer 1

No

Answer 2

Yes