8.1. Frangment ER

Calculate relative binding free energy between protein and ligand using Fragment ER method.

Purchase of add-on is necessary for using.

We use NAMD for molecular dynamics solver.

8.1.1. Fragment ER window

File menu

New Project: Initialize the project.
Open Project: Open the project.
Save Project: Overwrite and save the project.
Save Project As: Save the project with a name.
Close: Close the Fragment ER window.

MD menu

NAMD Keywords Setup: Open NAMD Configure window.
Run NAMD: Run NAMD locally.
Run NAMD On Remote Server: Open Remote Job Submission window for NAMD execution on remote server.
Edit .log File: Open the log file at NAMD execution with a text editor.
Energy Plot: Draw graph of energy change from log file at NAMD execution.
Import NAMD Trajectory: Open the MD trajectory.
Clear NAMD Output Files: Delete the output file made by NAMD execution. Delete RunNAMD.bat, RunNAMD.log, various dcd, log, coor, namd, vel, xsc, xst files etc ..

Analysis menu

Calculate Free Energy: Calculate free energy.
Edit .log File: Open the log file at free energy calculation with a text editor.
Import Result: Import the free energy calculation result and display it in Result display window.
Clear Analysis Output Files: Delete the output file made by free energy calculation. Delete FreeEnergy.sh, FreeEnergy.log, calc_PdP_kai2.out, parameters_fe file, refs, soln folder etc.

Tools menu

Preferences: Preferences window is displayed.

Solution

Specify PDB file of solution type by clicking … button. If more than one ligand molecule is present, designate the ligand molecule. Ligand molecules are displayed in the view.

Set Core

By clicking on the atom of the fragment part from the initial ligand and clicking the Set Core button, the remaining part is set as the mother nucleus.

Add

After selecting a new fragment with a combo box, click the Add button to add the ligand with the new fragment added to the mother nucleus to the final ligand list.

Configure

Fragment ER setting window is displayed.

Check

It checks whether atom types of mother nuclear parts of various ligands match. At the same time it generates force field of ligand.

Setup

Generate input file (PDB, PSF file) of NAMD.

Close

Close the Fragment ER window.

8.1.2. Fragment ER setting window

Set up Fragment ER calculation. The setting contents are recorded in the project file.

Solvation

Drop water and solvate for In-protein: Set whether water molecules should be rearranged by calculation of In-protein system. If you do not do this, water molecules of the solution system you read will be used as a solvent. If this is not done, periodic boundary cells must be set.
Drop water and solvate for In-aqua: Set whether water molecules are rearranged by calculation of In-aqua system. If you do not do this, water molecules of the solution system you read will be used as a solvent. If this is not done, periodic boundary cells must be set.
Distance from solute to cell boundary: Specify the distance from the solute to the periodic border cell.

Forcefield for Ligands

Select the type of force field to use for the ligand.

N-terminal modification

Specify N-terminal modification of protein.

C-terminal modification

Specify the C-terminal modification of the protein.

Import trajectory Interval

Specify how often to thin out when trajectory is imported.

ERmod

# of bins for binding energy: Specify the division number of binding energy.
# of insersions for solute (maxins): ermod Specify maxins at runtime.
# of division of the simulation (engdiv): ermod Specify engdiv at run time.
# of OpenMP threads (for local run): ermod Specifies the number of OpenMP threads on local execution.
# of MPI processes (for remote run): ermod Specifies the number of MPI processes at remote execution.

OK

Save the settings and close the window.

Cancel

Close the window without saving the setting.

8.1.3. NAMD Configure window

Set up MD calculation by NAMD. The setting contents are recorded in the project file. Select the system to be calculated with the check box.

Conf

Set the input file for NAMD calculation of each system.

numdcd: Specify the output interval of the trajectory.
numlog: Specify the output interval of the log file.
temperature: Specify the temperature. In the equilibrium calculation of In-protein, it is the temperature at the first stage of the stage temperature rise.
timestep: Specify the time step of 1 step of MD.
numstep: Specify the number of MD steps.

Number of Therad

Specify the number of threads when NAMD is executed.

Generate Conf Files

Output the input file (namd file).

Run

Output the input file and execute NAMD locally.

Close

Close the NAMD Configure window.

Load Default

Load default setting condition.

Save Default

Save the current setting condition as the default setting.

Reset Default

The default setting condition is reset to the initial state.

8.1.4. Result display window

A summary of the results is displayed in Summary. A graph of the energy distribution function is displayed. You can select which system to display.

log: Open the log file with a text editor.
Excel: Save the data displayed in the graph as a CSV file and open it with the application.
Close: Close the result display window.

8.1.5. Preferences window

NAMD Path: Set the path of the NAMD executable file.
Protein Topology Path: Specify the protein topology file.
Protein parameter Path: Specify the protein parameter file.