normal dna-tutorial-martinize-dna.py error

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3 years 3 months ago #8780 by bayıl
dna-tutorial-martinize-dna.py error was created by bayıl
I am trying to dna-tutorial.
1. Unpack the tutorial files you downloaded (it expands to na-tutorials).

$ tar -xvzf na-tutorials_20170815.tar
$ grep -v HETATM 1bna.pdb > 1BNA-cleaned.pdb
$ gmx editconf -f 1BNA-cleaned.pdb -o 1BNA-cleaned.gro.
İt has been succesfully created.But,when I give the command "$ python martinize-dna.py -dnatype ds-stiff -f 1BNA-cleaned.gro -o cg-dna.top -x cg-1bna.pdb"
İt gives error "Command 'python' not found, did you mean:command 'python3' from deb python3 ,command 'python' from deb python-is-python3
please how to fix ?

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3 years 3 months ago #8781 by bart
Replied by bart on topic dna-tutorial-martinize-dna.py error
Dear Bayil,

Python is a programming language and compiler which is used to run the python scripts *.py. Depending on you operating system it might or might not be linked in your PATH or installed. If you are using Ubuntu or some other form of Linux you can try python3 which is the new version. Most people source python3 as python.

Cheers,

Bart

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3 years 3 months ago #8783 by peterkroon
Replied by peterkroon on topic dna-tutorial-martinize-dna.py error
Although Bart is correct, I'm not completely sure martinize works with python3. Definitely give it a try, but if it doesn't work you'll need to install Python 2. Depending on you OS you can do e.g. `apt install python`.

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