Tool.py

Hello!

Pasindu has developed tool.py, which can be used to calculate interaction energies in a couple of different ways. It is much more customizable than gRINN and easier to use than NAMD Energy. As long as your system has two chains (labelled Chain A and Chain B; more functionality coming later), it will work with tool.py.

How to install (Mac/Linux):

1. Download tool.py.

2. If you'd like, open tool.py in a Python or text editor and change the path after NAMD2_LOCATION to your NAMD file's path.

3. cd to the directory where tool.py was downloaded (for instance, cd ~/Downloads on Mac)

4. Type sudo cp tool.py /usr/local/bin/tool && sudo chmod +x /usr/local/bin/tool

5. Enter your login password.

Tool.py is not supported on Windows. Please use a Linux-capable lab laptop if your computer runs Windows.

How to use:

Once the tool is installed, follow these instructions to use it.

1. Copy your .pdb, .psf, and .dcd files to a new directory. Copy the parameter file to that directory as well.

2. Open a terminal and cd to that directory.

3. Enter tool. If you did not reset your NAMD executable's path during installation, enter tool --namd filepathhere instead.

4. Verify that the files listed are the correct files. Then, select an option.

5. Option 1, chain-chain: This option is used to determine the interaction energies (frame-by-frame) between the entirety of both chains. This is a relatively short task. When finished, you'll have an output.csv file where you can see the results. Rename this file to Total Interaction Energy.csv.

6. Option 2, chain-residue: This option is used to determine the interaction energies (frame-by-frame) between each individual residue of chain A (or a smaller selection) against all of chain B. This can take a little longer. When you select option 2, you'll need to input the residue IDs as min max with a space between. If you're computing all of sACE2 against the receptor binding domain, you would enter 21 615 when prompted (or you could press enter to do all of them). When finished, output.csv will show you the results. Rename this file to Residue Interaction Energy.csv.

7. If you get an error, be sure to delete temp.pdb from the folder before trying again. Otherwise, you'll get an error on startup.

8. Copy plot.py and script.py to the directory. Open a Terminal window and cd to that directory. Run python3 plot.py.

9. Open script.py for editing. Near the bottom, change sace2-rbd-ns1-2.pdb to the correct system name. In the terminal, run python3 script.py.

10. Create a text file (readme.txt) in the directory using the template. Upload the files listed in the readme to the Drive, and add a link to the containing folder to the COVID-19 Progress page.