Name

SQMPC

Software

Maestro 10.4
MOPAC 2016
AMBER 16

Parameters

PM7
1.5 ns

Method

Firstly, We used Maestro to get the docking pose of all those ligands, then we recalculate the atomic charge of protein and ligand using semi-empirical quantum mechanics methods (PM7), to replace the common AMBER ff03 charge.After that ,weperformed 1.5 ns MD on those systems.GAFF and AMBER FF03 force field parameters were assigned to the all ligands and protein,respectively.With MD simulation trajectories, the absolute ĶĪG can be calculated with SIE method based on the 1.0-1.5ns MD trajectories.

Answer 1

No

Name

SQMPC

Software

Maestro 10.4

System Preparation Parameters

Assumed pH 7.0

System Preparation Method

We used Maestro's prepwizard to add hydrogens using default parameters
and an assumed pH of 7.0.

Pose Prediction Parameters

Parameters: 1.5 ns

Pose Prediction Method

we performed 1.5 ns MD on those docking pose.

Answer 1

NO

Answer 2

NO