A4. Working with Proteins

In this section, we use a protein model as example to use TEAMFF.

Models built using external software may need to be modified before assigning a force field. In this lesson, we will work on one example. A protein1.mol2 file is provided with this tutorial. The model does not have hydrogen atoms, so we will assign hydrogen atoms first.

1. Under “tutorials” project, right-click on “tutorialA4_Protein” folder and select add model command in the pulldown menu. In the "Open" dialog, set "Files of type" to “MOL2 Files (*.mol2)” and select “protein1.mol2”. Click Open to load both models.

2. In the Project Navigator, click the newly added model to view it in the main screen. The model does not have hydrogen atoms. Click Add Hydrogen button on the tool bar to add hydrogen atoms automatically.

3. Click TEAMFF/Admin command. Select “AMBER” force field type and “AMBER-General” force field. The, select protein1 in the Project Navigator and click TEAMFF/Assign command. Note that the selected force field, model (protein1), and output force field are listed in the dialog. Click OK to assign force field parameters. When the job is complete, a force field table appears. The force field type is AMBER and the typing rule is “Composed”, which means atom types have been successfully assigned. PREPARE THE MODEL

4. Select “Protein1.msd” from the Project Navigator and click Build/Charge Group. Set “Allow charge crossing a bond” parameter to “0.1” and click Execute. The text area shows the results indicating the largest group has 7 atoms. To define small charge group is essential. The groups do not have to be charge neutral, but the size may be an issue. For example, if the group is too large, GROMACS may fails.

5. Because hydrogen atoms were automatically added, the structure is not relaxed. If the configuration is submitted to GROMACS or LAMMPS, the simulation may fail. Therefore, we should relax this configuration first. To do so, select “Protein1.msd” and open Simulation/Optimization:

Click on “Nonbond Energy”, which opens the following dialog:

Select “Group Cutoff” and leave other options unchanged. Click OK to close this dialog. Click OK again in the “Optimization” dialog and watch as the energy value drops. When the job is done, the optimized model will be saved to a subfolder named “protein1_OPT”.

7. Now we are ready to submit a job to GROMACS. Click “protein1.msd” from the “protein1_OPT” folder. Make sure the force field is still associated and select Simulation/GROMACS command.

8. Using the default options, set the simulation steps to small numbers (e.g. 1000 steps), and click OK to start the job. The trajectory file will be saved as “protein1.dta”.

9. When the job is complete, a notice will pop up and a subfolder named “protein1_GROMACS” will be placed under the folder in which the job is started. Double-click on the files in this subfolder to see the results of the simulation. Open the “protein1_GROMACS” folder, right-click select Import, set the file type to “GROMACS Trajectory File”, and select “protein1.dta” to load the trajectory file into protein1.dta.

10. Select “protein1.msd” and protein1.dta, then click Simulation/Trajectory Viewer to see the trajectory.