# Using the Protein MD Setup tutorial using BioExcel Building Blocks (biobb) --AmberTools package version-- with Amber installed frome sources

**URL:** <https://ask.bioexcel.eu/t/using-the-protein-md-setup-tutorial-using-bioexcel-building-blocks-biobb-ambertools-package-version-with-amber-installed-frome-sources/4702>\
**Category:** BioBB\
**Created:** [November 26, 2023, 6:40pm UTC](https://ask.bioexcel.eu/t/using-the-protein-md-setup-tutorial-using-bioexcel-building-blocks-biobb-ambertools-package-version-with-amber-installed-frome-sources/4702 "2023-11-26T18:40:52Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![saverio](https://avatars.discourse-cdn.com/v4/letter/s/dbc845/32.png) [@saverio](https://ask.bioexcel.eu/u/saverio)\
**Post date:** [November 26, 2023, 6:40pm UTC](https://ask.bioexcel.eu/t/using-the-protein-md-setup-tutorial-using-bioexcel-building-blocks-biobb-ambertools-package-version-with-amber-installed-frome-sources/4702/1 "2023-11-26T18:40:52Z")

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Hi,  
I’ve used the Protein MD Setup tutorial using BioExcel Building Blocks (biobb)  
–AmberTools package version–  
following the instructions:  
git clone https://github.com/bioexcel/biobb\_wf\_amber\_md\_setup.git  
cd biobb\_wf\_amber\_md\_setup  
conda env create -f conda\_env/environment.yml  
conda activate biobb\_AMBER\_MDsetup\_tutorials  
jupyter-notebook biobb\_wf\_amber\_md\_setup/notebooks/mdsetup/biobb\_amber\_setup\_notebook.ipynb

I have also installed AmberTools23 and Amber22 on the same system ( UBUNTU 22.04 ) compiling both from the sources with -DCUDA=TRUE -DOPENMP=TRUE.

It is possible to run the notebook using the sander and pmemd that have been compiled from the  
sources so to use all threads and the gpu?

I have run the notebook and analyzing htop I have noticed that only one thread has been used during all the processing and I guess that the gpu was never used.

Thanks.

Saverio

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**Author:** ![adam.hospital](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/adam.hospital/32/151_2.png) [@adam.hospital](https://ask.bioexcel.eu/u/adam.hospital)\
**Post date:** [November 27, 2023, 10:17am UTC](https://ask.bioexcel.eu/t/using-the-protein-md-setup-tutorial-using-bioexcel-building-blocks-biobb-ambertools-package-version-with-amber-installed-frome-sources/4702/2 "2023-11-27T10:17:19Z")

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Hi Saverio,

yes, for this cases you can use the `binary_path` property, which lets you use a locally installed software instead of the one packaged with the BioBB module. You’ll need to first identify the corresponding binaries (e.g. pmemd.CUDA or pmemd.MPI).

You should also change the `sander_mdrun` block for the `pmemd_mdrun` block if using pmemd binary instead of the sander one.

Hope this helps!

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<div class="post-metadata">

**Author:** ![saverio](https://avatars.discourse-cdn.com/v4/letter/s/dbc845/32.png) [@saverio](https://ask.bioexcel.eu/u/saverio)\
**Post date:** [November 27, 2023, 3:45pm UTC](https://ask.bioexcel.eu/t/using-the-protein-md-setup-tutorial-using-bioexcel-building-blocks-biobb-ambertools-package-version-with-amber-installed-frome-sources/4702/3 "2023-11-27T15:45:54Z")

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Ok.  
Thanks.

Saverio