# Membrane protein constant pH Amber

**URL:** <https://ask.bioexcel.eu/t/membrane-protein-constant-ph-amber/4072>\
**Category:** General Topics in Molecular Dynamics\
**Created:** [January 11, 2023, 3:16pm UTC](https://ask.bioexcel.eu/t/membrane-protein-constant-ph-amber/4072 "2023-01-11T15:16:19Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![mhk](https://avatars.discourse-cdn.com/v4/letter/m/b3f665/32.png) [@mhk](https://ask.bioexcel.eu/u/mhk)\
**Post date:** [January 11, 2023, 3:16pm UTC](https://ask.bioexcel.eu/t/membrane-protein-constant-ph-amber/4072/1 "2023-01-11T15:16:19Z")

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Hi!  
I want to use “biobb\_amber\_CpHMD\_notebook”, to prepare my system which is an ion channel for running CpHMD with Amber.

My questions are:

1. Is it possible to embed the protein in membrane with biobb in some step? or use the already prepared membrane embedded solvated system from CHARMM-GUI as an input? If so, to prepare the initial parameters and topology, which terms should be added to include the forcefields of ions and lipids to be taken into consideration. or what are the required changes in the steps.

Thank you in advance  
Regards  
Mahdi

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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:** [January 13, 2023, 7:53am UTC](https://ask.bioexcel.eu/t/membrane-protein-constant-ph-amber/4072/2 "2023-01-13T07:53:13Z")

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Dear Mahdi,

I’m afraid there’s no module in the BioBB library at this time to embed the protein in membrane.

Using the CHARMM-GUI to prepare the system and use the results as an input for the notebook should be possible, although you will need to modify the workflow. Sorry I am not familiar with the outputs of the server, so I can not tell you what exactly needs to be modified. About the force fields, it should be enough to add them to all the leap building blocks (leap\_gen\_top, leap\_solvate, leap\_add\_ions), using the `force_field` property and/or the input parameters `input_params_path` and `input_source_path`.

If you try it and find problems, please contact us again and we will try to help you during the process.

Thanks for your interest in our tools!

Regards,

-Adam-