[gmx-users] Embedding Protein into lipid bilayer

[Catarina A. Carvalheda dos Santos]

Hi Ali,

First create the topology for the protein alone using pdb2gmx.

Then, and if you already have a pre-equilibrated membrane patch, perform
the protein alignment and insertion into the membrane. There are several
ways to do this (see below).

Align the protein with the membrane:
- manual procedure/visual inspection (not recommended)
- based on OPM database information
- automatic tools: CHARMM-GUI, CELLMICROCOSMOS or LAMBADA

Insert the protein into the membrane:
- Alchembed Jefferys_2015_JCTC
<http://pubs.acs.org/doi/abs/10.1021/ct501111d>
- CHARMM-GUI
- CELLMICROCOSMOS
- INFLATEGRO2Schmidt_2012_JCIM
<http://pubs.acs.org/doi/abs/10.1021/ci3000453>

I recommend the LAMBADA/INFLATEGRO2 combination.

Keep in mind that automatic tools might fail, so you should always check
the output files at each step.

After this, add the lipids to the topology file (number of lipid molecules
and lipid parameters) and proceed to solvation, adding ions, minimization,
equilibration and then production phase.

I'm not sure if this answers to your question, but I hope it helps anyway.

Cheers,

On 19 February 2016 at 08:33, <khourshaeishargh at mech.sharif.ir> wrote:

>
>
>
> Dear All
> During researching Internet, I found justin and Anirban&#39;s tutorial
> about embedding protein
> in lipid membrane. It was useful and I appreciate them but I had one
> question. as I understood, I should make some changes to protein pdb file
> ( 1r2h for Ex)
>  before using it in  pdb2gmx command or the GROMACS can&#39;t
> keep on and will be died with a fatal error ( something like adding cope
> to the ends of the protein ). could
> somebody please tell me what should I do ? by the way I found out that
> Justin&#39;s
> tutorial do something with xleap amber on the pdb file.
> Please tell me how specifically I should revise my protein pdb file.
>
> best regards
> Ali khourshaei shargh (khourshaeishargh at mech.sharif.ir)
> Department of Mechanical Engineering
> Sharif University of Technology, Tehran, Iran
>
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-- 
Catarina A. Carvalheda

PhD Student
Computational Biology Division
SLS & SSE
University of Dundee
DD1 5EH, Dundee, Scotland, UK