# PMX tutorial free energy sign

**URL:** <https://ask.bioexcel.eu/t/pmx-tutorial-free-energy-sign/4309>\
**Category:** pmx\
**Created:** [May 11, 2023, 11:36am UTC](https://ask.bioexcel.eu/t/pmx-tutorial-free-energy-sign/4309 "2023-05-11T11:36:04Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Hryhory\_Sinenka](https://avatars.discourse-cdn.com/v4/letter/h/a9adbd/32.png) [@Hryhory\_Sinenka](https://ask.bioexcel.eu/u/Hryhory_Sinenka)\
**Post date:** [May 11, 2023, 11:36am UTC](https://ask.bioexcel.eu/t/pmx-tutorial-free-energy-sign/4309/1 "2023-05-11T11:36:04Z")

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Dear Dr. Gapsys,

This is a very simple question, just to resolve some possible misinterpretations.

In the 2020 Tutorial ([Ligand modification free energy calculations](http://pmx.mpibpc.mpg.de/summerSchool2020_tutorial2/index.html#contents)) in the very end there is a phrase “_**The calculated value is 0.26 kJ/mol, while the ITC value in the [publication (Table 1)](http://pmx.mpibpc.mpg.de/summerSchool2020_tutorial2/baum_2009_JMB_thrombin_ligands.pdf) is 0.4 kJ/mol.**_” Indeed, when I use the dhdl-output of the Tutorial’s authors ([http://pmx.mpibpc.mpg.de/lugano2019\_tutorial2/dhdl.tar.gz](http://pmx.mpibpc.mpg.de/lugano2019_tutorial2/dhdl.tar.gz)), I get the alchemical BAR dG for protein of 147.84 kJ/mol and for water of 147.58 kJ/mol and thus calculated ddG of 0.26 kJ/mol. But if I look in Table 1 of the mentioned publication, the binding free energy of lig\_1a is -31.3 kJ/mol and of lig\_5 is -31.7 kJ/mol. Considering that in the topology the state A corresponded to lig\_1a and state B corresponded to lig\_5, I would say that the experimental value to compare with is -31.7 - (-31.3) = -0.4 kJ/mol, I mean has a different sign. What do you think?

This is just a more technical question about the sign, everything is still within the chemical accuracy here of course.

Thank you very much in advance!

Sincerely,  
Hryhory Sinenka, PhD student at Strasbourg University

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**Author:** ![bgroot](https://avatars.discourse-cdn.com/v4/letter/b/dc4da7/32.png) [@bgroot](https://ask.bioexcel.eu/u/bgroot)\
**Post date:** [May 11, 2023, 12:27pm UTC](https://ask.bioexcel.eu/t/pmx-tutorial-free-energy-sign/4309/2 "2023-05-11T12:27:39Z")

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Hi Hryhory,

yes, I would agree with your interpretation.

best

Bert