Hi..
I installed miniconda3 and then ambertools23 in linux in the virtual box. However when I try to work in my desired directory and run a command in the terminal, it says command not found.
I edited the .bashrc file as recommend in the internet, but the problem still exisists.(When I worked in gromacs, the same problem occured, but it was solved when the path was added in the .bashrc file)
Hope someone can provide me with a suitable solution.
Thanks in advance..😊
Navoda Wijesuriya
I understand that you're encountering a "command not found" error when trying to run commands related to ambertools23 in Linux. This issue can typically be resolved by ensuring that the necessary paths are correctly set. Here are a few steps you can try to fix this problem:
1. Verify the installation: First, double-check that ambertools23 is installed correctly. Confirm the installation path and ensure that the necessary binaries and scripts are present.
2. Check the PATH variable: Open the `.bashrc` file again and make sure that the installation directory of ambertools23 is added to the `PATH` variable. The line you added should resemble something like this:
```
export PATH=/path/to/ambertools23/bin:$PATH
```
Save the file and restart the terminal or run the command `source ~/.bashrc` to apply the changes.
3. Confirm the installation directory: Ensure that the installation directory you specified in the `.bashrc` file is accurate and matches the actual location of the ambertools23 installation.
4. Verify executable permissions: Check that the necessary files in the ambertools23 directory have executable permissions. You can do this by running the command `ls -l /path/to/ambertools23/bin` and verifying that the files have the execute permission (e.g., `-rwxr-xr-x`).
5. Try using the full path: If the previous steps didn't resolve the issue, you can try running the commands using the full path to the executable. For example, instead of running `ambertools_command`, try running `/path/to/ambertools23/bin/ambertools_command`.
6. Reinstall ambertools23: If all else fails, it might be necessary to reinstall ambertools23. Remove the existing installation, then reinstall it following the provided instructions carefully.
Remember to substitute `/path/to/ambertools23` with the actual installation directory path on your system.
I hope one of these steps helps resolve the "command not found" error you're experiencing with ambertools23.
After a personal struggle with gromacs installation for 3 days as far as I remember, the best way to resolve environment path problems regarding gromacs commands and tools is to install gromacs via terminal in your linux distro
sudo apt-get install gromacs
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