[gmx-users] How to build a lipid bilayer in GROMACS?

[Justin A. Lemkul]

Anirban Ghosh wrote:
> Hi ALL,
> 
>  
> 
> I have a protein pdb file. I want to put this protein molecule in a 
> lipid bilayer using GROMACS. I shall be glad if anyone can kindly tell 
> me how to build a lipid bilayer in GROMACS and how to embed the protein 
> in it to get the final pdb of the entire system. Thanks a lot.
> 
>  

There are several options for the lipid bilayer:

1. Obtain the coordinates from a freely-available configuration (there are many 
investigators who offer their coordinates for free)
2. Obtain the .pdb file for a single molecule, and use genconf to create a 
lattice of molecules (and even apply random rotations).  Build two leaflets, 
solvate, and equilibrate for a very long time.
3. If you have a bilayer with a similar lipid, write a script that can change 
atom names/add or delete atoms to generate the new lipid.

The caveat to all of these options is that you need proper parameters for the 
lipid of interest.  If such parameters do not exist yet, you have your work cut 
out for you.  If parameters have already been developed, then likely the 
configurations for the bilayer exist online somewhere as well.

To build the system, there are also a couple of options:

1. The InflateGRO script from Peter Tieleman's site, which I utilize in my 
membrane protein tutorial:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html

2. Orient your protein properly and solvate using genbox, with the bilayer 
configuration as the solvent.  This procedure can be hit-or-miss, as sometimes 
there can be atomic overlap in the output configuration, or alternately, voids 
between the protein and lipids.

-Justin

> 
> Regards,
> 
>  
> 
>  
> 
> Anirban Ghosh
> 
> Grade Based Engineer
> 
> Bioinformatics Team
> 
> Scientific & Engineering Computing Group
> 
> Centre for Development of Advanced Computing
> 
> Pune, India
> 
>  
>  
> *Anirban Ghosh*
> *Grade Based Engineer
> Bioinformatics Team
> Centre for Development of Advanced Computing (C-DAC)
> Pune, India
> *
> 
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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