# Free Energy Calculation from DCD Trajectory?

**URL:** <https://help.galaxyproject.org/t/free-energy-calculation-from-dcd-trajectory/8532>\
**Category:** usegalaxy.eu support\
**Tags:** comp-chemistry\
**Created:** [August 25, 2022, 5:24pm UTC](https://help.galaxyproject.org/t/free-energy-calculation-from-dcd-trajectory/8532 "2022-08-25T17:24:28Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![christos-efthymiou](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/christos-efthymiou/32/3125_2.png) [@christos-efthymiou](https://help.galaxyproject.org/u/christos-efthymiou)\
**Post date:** [August 25, 2022, 5:24pm UTC](https://help.galaxyproject.org/t/free-energy-calculation-from-dcd-trajectory/8532/1 "2022-08-25T17:24:28Z")

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I would like to calculate the free energy of binding of a protein-protein complex from a NAMD simulation. On Galaxy I can see an MMPBSA/MMGBSA tool, but this seems to require AMBER prmtop inputs. Are there any tools on Galaxy that can be used to calculate the free binding energy from a dcd trajectory?

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**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [September 21, 2022, 9:19pm UTC](https://help.galaxyproject.org/t/free-energy-calculation-from-dcd-trajectory/8532/2 "2022-09-21T21:19:14Z")

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Cross-posted here: [https://www.researchgate.net/post/How\_do\_you\_calculate\_the\_free\_binding\_energy\_of\_a\_protein-protein\_interaction\_from\_a\_molecular\_dynamics\_simulation](https://www.researchgate.net/post/How_do_you_calculate_the_free_binding_energy_of_a_protein-protein_interaction_from_a_molecular_dynamics_simulation)

Galaxy resources:

**Tools**

- Search with keywords or review under the `ChemicalToolbox` tool group at usegalaxy.\* servers
- Or, use the domain-specific server [ChemicalToolbox - Galaxy Community Hub](https://galaxyproject.org/use/chemicaltoolbox/)

**Tutorials**

> **[Galaxy Training: Computational chemistry](https://training.galaxyproject.org/training-material/topics/computational-chemistry/)**
>
> Modelling, simulation and analysis of biomolecular systems

**Help**

Each tool form has a help section at the bottom. Upstream tools or example inputs are usually referenced, and that is true for the `MMPBSA/MMGBSA` tool.