While running g_mmpbsa, I gave commend in Linux Ubuntu,
python MmPbSaStat.py -m energy_MM.xvg -p polar.xvg -a apolar.xvg (I have all python files)
However it is telling Python command not recognized. Earlier I did it other system, but in the new computer this issue is happening
Make sure you have Python installed on your system and it's available on your PATH. If you are using Anaconda or something similar, it will come with a launcher that sets up your environment variables for that session, and you will need to open that before running your command. If you are using regular Python, and you are sure that this will be the only version of Python you will want on your system, you can just reinstall Python and check the option "add Python to PATH".
If you have only python3 installed you might want to install : python-is-python3, but if you want python2 and python3 installed you need to specify which version you want to use.
In a terminal try to run python3 , if that works then install : sudo apt install python-is-python3
Alexander Liptak Hii thanks for the response. I am using Ubuntu. I installed both Python 2 and 3. I am not very expert in Linux command line, but in the earlier system I was able to run it, however in the new one I am failing, and I forgot what I did there. But path how to add I am not clear.
Patrick Charron-Morneau Hii, thanks. This command I dint try. But I gave command sudo apt install python2 and python3 separately and in the terminal I can see Python3 version, when I checked. Tomorrow I am going to try your suggested command next. I tried like python3 MmPbSaStat.py -m energy_MM.xvg -p polar.xvg -a apolar.xvg, then it is askiong for 'numpY' when I tried installing numpy not working
if you have python2 and python3 installed , you will have to install packages in the python version you want.
I only know how to install python packages with pip.
If you need to install package for python3 you will need to use pip3.
If you don't need python2 ( which is the case in most situation ) install python-is-python3 and you will have to stop worrying about versions and make things a lot easier for you.
python-is-python3 will work for sure for ubuntu 20 to 22 and probably 18
you should install python packages in Linux operating system to use the python commands
Anish Nag Complete workflow can be found here Article Gmx_qk: An Automated Protein/Protein-Ligand Complex Simulati...
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