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How to run do_dssp command (mkdssp) in Gromacs 2022?

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How to run do_dssp command in Gromacs 2022?

In the latest version of GROMACS (2022) [1], there are some issues regarding the gmx do_dssp command. Apparently, this command either does not run displaying a fatal error, or if it runs then it does not read any frame from MD simulation files. In this article, we are going to run the same command for GROMACS 2022.

We do not invoke the dssp program in this command. We need to point the $DSSP to the executable. In the latest version of GROMACS, we need to point it to mkdssp. You don’t have to install mkdssp separately. It is installed with the dssp program [2]. Let’s see how we can do that.

1. Remove the installed dssp program (if any)

$ sudo apt-get --purge remove dssp

It should remove the installed dssp package. Now check whether it is still there.

$ which dssp

If it displays a path then go to that directory and remove it. For example, if it shows /usr/local/bin/dssp, then move inside this directory and remove it using the following command. You can see a dssp file there.

$ cd /usr/local/bin/

$ sudo rm -rf dssp

If there is another file named mkdssp, then remove it too.

$ sudo rm -rf mkdssp

Now you have completely removed dssp from your system.

2. Re-install dssp

Now let’s reinstall dssp using the following command.

$ sudo apt-get install dssp

3. Get the path of the executables

Let’s get the path of the dssp executable.

$ which dssp

It would display /usr/bin/dssp or another similar path.

Now, let’s get the path of the mkdssp executable.

$ which mkdssp

It would display /usr/bin/mkdssp or another similar path.

4. Pointing DSSP to mkdssp

After successful installation, let’s point $DSSP to mkdssp to run the gmx do_dssp command.

$ export DSSP=/usr/bin/mkdssp

After that, you can run the gmx do_dssp command. It will work.

5. Adding it to the path

You can add this command to your bashrc file in order to save you from the trouble of running the same command over and over every time you open a new terminal. To do that, open the bashrc file and add this command at the end of the file and then save it as shown below.

$ sudo gedit ~/.bashrc

Paste this export command at the end of the file and save.

$ source ~/.bashrc


References

  1. Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX1, 19-25.
  2. Frishman, Dmitrij, and Patrick Argos. “Knowledge‐based protein secondary structure assignment.” Proteins: Structure, Function, and Bioinformatics 23.4 (1995): 566-579.

Dr. Muniba is a Bioinformatician based in New Delhi, India. She has completed her PhD in Bioinformatics from South China University of Technology, Guangzhou, China. She has cutting edge knowledge of bioinformatics tools, algorithms, and drug designing. When she is not reading she is found enjoying with the family. Know more about Muniba

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Bioinformatics Programming

Extracting first and last residue from helix file in DSSP format.

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Extracting first and last residue from helix file in DSSP format.

Previously, we have provided a tutorial on using dssp_parser to extract all helices including long and short separately. Now, we have provided a new python script to find the first and last residue in each helix file. (more…)

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