# Ligand Binding Free Energies with PMX

**URL:** <https://ask.bioexcel.eu/t/ligand-binding-free-energies-with-pmx/2532>\
**Category:** BioBB\
**Created:** [November 3, 2020, 7:32pm UTC](https://ask.bioexcel.eu/t/ligand-binding-free-energies-with-pmx/2532 "2020-11-03T19:32:21Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![dburns](https://avatars.discourse-cdn.com/v4/letter/d/a88e57/32.png) [@dburns](https://ask.bioexcel.eu/u/dburns)\
**Post date:** [November 3, 2020, 7:32pm UTC](https://ask.bioexcel.eu/t/ligand-binding-free-energies-with-pmx/2532/1 "2020-11-03T19:32:21Z")

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Is there an available tutorial for ligand binding free energy calculations? Maybe I should try to apply the available pmx tutorials to a biobb format.

Thank you,

Dan

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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 4, 2020, 7:53am UTC](https://ask.bioexcel.eu/t/ligand-binding-free-energies-with-pmx/2532/2 "2020-11-04T07:53:12Z")

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Hi Dan,

what do you mean by ligand binding free energy calculations? We are going to generate a BioBB demonstration workflow, hopefully soon, following the available pmx tutorial about [ligand modification for free energy calculations](http://pmx.mpibpc.mpg.de/summerSchool2020_tutorial2/index.html). But we were waiting for the new pmx Python3 version, which was released two weeks ago. Now we have a [Conda package](https://anaconda.org/bioconda/pmx_biobb) with this new pmx version, and we have adapted the pmx building blocks to the new syntax ([biobb\_pmx python3 branch](https://github.com/bioexcel/biobb_pmx/tree/python3/biobb_pmx)).  
With this new modifications, building reproducible workflows integrating Gromacs and pmx will be easier. The next one in the roadmap is the ligand modification one, although we’ll need to generate new building blocks for the new pmx functionalities that are not yet integrated in the BioBB library.

Of course, you are very welcome to help us on this task! Remember we have a [Build your own BioBB tutorial](http://mmb.irbbarcelona.org/biobb/build) in the BioBB web portal! 🙂

Will keep in contact!

Regards,

-Adam-

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**Author:** ![vgapsys](https://avatars.discourse-cdn.com/v4/letter/v/7993a0/32.png) [@vgapsys](https://ask.bioexcel.eu/u/vgapsys)\
**Post date:** [November 12, 2020, 10:13am UTC](https://ask.bioexcel.eu/t/ligand-binding-free-energies-with-pmx/2532/3 "2020-11-12T10:13:12Z")

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Hey Dan,

if you are interested in relative free energy calculations you can find a tutorial here: [https://github.com/deGrootLab/pmx/tree/develop/tutorials](https://github.com/deGrootLab/pmx/tree/develop/tutorials)

Note, for now you would need to use the “develop” branch of pmx.

Vytas