[gmx-users] Embedding Protein into lipid bilayer
Catarina A. Carvalheda dos Santos
c.a.c.dossantos at dundee.ac.uk
Fri Feb 19 11:21:02 CET 2016
You can also use g_membed (a GROMACS tool) for the protein insertion. In
the latest GROMACS versions g_membed is part of the mdrun tool (-membed
flag). The reference is Wolf_2010_JC
g_membed is easily combined with LAMBADA as well.
On 19 February 2016 at 10:15, Catarina A. Carvalheda dos Santos <
c.a.c.dossantos at dundee.ac.uk> wrote:
> 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
> - CHARMM-GUI
> - CELLMICROCOSMOS
> - INFLATEGRO2Schmidt_2012_JCIM
> 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.
> On 19 February 2016 at 08:33, <khourshaeishargh at mech.sharif.ir> wrote:
>> Dear All
>> During researching Internet, I found justin and Anirban'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'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
>> 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
Catarina A. Carvalheda
Computational Biology Division
SLS & SSE
University of Dundee
DD1 5EH, Dundee, Scotland, UK
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