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Trouble plotting free energy landscape diagram

Nubia Prates
Posted 12 years ago

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?

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POSTED BY: Nubia Prates
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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
POSTED BY: Sean Clarke
Nubia Prates
Nubia Prates
Posted 12 years ago

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.

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POSTED BY: Nubia Prates
POSTED BY: Sean Clarke
Nubia Prates
Nubia Prates
Posted 12 years ago

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".
POSTED BY: Nubia Prates
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