# Membrane simulation

**URL:** <https://ask.bioexcel.eu/t/membrane-simulation/410>\
**Category:** GROMACS\
**Created:** [July 17, 2017, 1:10pm UTC](https://ask.bioexcel.eu/t/membrane-simulation/410 "2017-07-17T13:10:20Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![HosseinLanjanian](https://avatars.discourse-cdn.com/v4/letter/h/dec6dc/32.png) [@HosseinLanjanian](https://ask.bioexcel.eu/u/HosseinLanjanian)\
**Post date:** [July 17, 2017, 1:10pm UTC](https://ask.bioexcel.eu/t/membrane-simulation/410/1 "2017-07-17T13:10:20Z")

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Dear All Hi  
I am working on a membrane protein. I created a membrane using VMD “membrane builder” and merged it with the protein pdb file by “Merge Structures” of VMD, for the rest of works I tried to use gromacs. My idea is to modify gromos53a6 and such that creates the protein-membrane complex topology file. I used the following tutorial:  
KALP-15 in DPPC - Bevan Lab - Virginia …  
But when I run pub2gmx command, the following error is appeared:  
Residue POPC not found in residue topology database.  
Do you have any idea?

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**Author:** ![scinikhil](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/scinikhil/32/66_2.png) [@scinikhil](https://ask.bioexcel.eu/u/scinikhil)\
**Post date:** [July 21, 2017, 9:10am UTC](https://ask.bioexcel.eu/t/membrane-simulation/410/2 "2017-07-21T09:10:44Z")

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You have to provide the topology file for your membrane which is POPC.

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**Author:** ![HosseinLanjanian](https://avatars.discourse-cdn.com/v4/letter/h/dec6dc/32.png) [@HosseinLanjanian](https://ask.bioexcel.eu/u/HosseinLanjanian)\
**Post date:** [July 22, 2017, 3:40am UTC](https://ask.bioexcel.eu/t/membrane-simulation/410/3 "2017-07-22T03:40:28Z")

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thank you scinikhil  
But, I think, to this aim the lipid.rtp file is needed and I can not find it for gromos53a6 which the tytorial is based on.  
fortunatly, I found lipids-AMBER-POPC-joakim-v2 pakage that contains all necessary files for lipids such as lipid.rtp, atomtypes.atp, forcefield.itp and fnonbonded.itp. so I combined this files with the corresponding files in the amber99sb-ildn force fileds and run the md as a normal method using this new forcefield.  
every thing sounds good.  
I would like to know is it right? Are have the same experience?

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**Author:** ![Andrea\_Spitaleri](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/andrea_spitaleri/32/37_2.png) [@Andrea\_Spitaleri](https://ask.bioexcel.eu/u/Andrea_Spitaleri)\
**Post date:** [July 24, 2017, 8:22am UTC](https://ask.bioexcel.eu/t/membrane-simulation/410/4 "2017-07-24T08:22:56Z")

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Hi,  
you can think to use BiKi Life Sciences to build your membrane-protein easily. Have look to [www.bikitech.com](http://www.bikitech.com)  
If you need an academia license you can contact me in private.  
Best  
and