AMBER/MMPBSA/ELIE
Amber method 2
Assumed pH 5.0
Typical simulation time per MD: 10 ns
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.
No
AMBER Method 2
Amber
Assumed pH 5
Tautomers considered
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.
MD simulations
MD simulations with explicit water molecules.
No
Yes