Trouble plotting free energy landscape diagram

Questions
,
1

I tried to plot free energy landscape by using the script (attached), using Mathematica from linux terminal: ./FEL.nb but it did not plot and I see the error message below :

./FEL.nb: linha 1: average-structure.pdb: comando não encontrado
./FEL.nb: linha 3: average-structure.pdb: comando não encontrado
./FEL.nb: linha 4: average-structure.pdb: comando não encontrado
./FEL.nb: linha 6: average-structure.pdb: comando não encontrado
./FEL.nb: linha 8: *CacheID:: comando não encontrado
./FEL.nb: linha 9: average-structure.pdb: comando não encontrado
./FEL.nb: linha 10: NotebookFileLineBreakTest: comando não encontrado
./FEL.nb: linha 11: NotebookFileLineBreakTest: comando não encontrado
./FEL.nb: linha 12: NotebookDataPosition[ 157, 7]: comando não encontrado
./FEL.nb: linha 13: NotebookDataLength[ 13755, 298]: comando não encontrado
./FEL.nb: linha 14: NotebookOptionsPosition[ 13198, 278]: comando não encontrado
./FEL.nb: linha 15: NotebookOutlinePosition[ 13615, 294]: comando não encontrado
./FEL.nb: linha 16: CellTagsIndexPosition[ 13572, 291]: comando não encontrado
./FEL.nb: linha 17: WindowFrame-: comando não encontrado
./FEL.nb: linha 19: average-structure.pdb: comando não encontrado
./FEL.nb: linha 276: fim do arquivo inesperado enquanto procurava por ``’
./FEL.nb: linha 308: erro de sintaxe: fim prematuro do arquivo

Can anyone help me?

2

Notebook files aren’t normally executable. Have you ever made a Mathematica script before?
If not, please take a look at the documentation below and try making some of the example scripts mentioned in the tutorial. Do they example/tutorial mathematica scripts work for you?

http://reference.wolfram.com/mathematica/tutorial/MathematicaScripts.html

3

Thank you for your help. I understand how it works, but now when I try to generate the graphs the following error message appears: Could not process unknown packet “Graphics3D”.

4

It’s hard to tell what the issue might be without seeing the script. If you are generating graphics, this requires the front end and cannot be run in the Mathematica kernel by itself.

Usually when working with graphics and images in the kernel, you have to run the code in UsingFrontEnd (http://reference.wolfram.com/mathematica/ref/UsingFrontEnd.html)

5

The script this attached. I was running the code in FrontEndExecute [%], but When I used the code that you recommended me the only thing I could see were the axis without the plot.