[gmx-users] How to incorporate WALP and KALP peptide in a Martini bilayer

Sanku M msanku65 at yahoo.com
Wed Oct 13 00:15:55 CEST 2010

Hi Tom,
  I hoped that I could self-assemble the bilayer around the peptide. But, the 
problem is how to do that. I am aware of the tutorial in the Martini website. 
But, in that case, they use genbox -ci option to insert certain lipid molecules 
in an EMPTY box. But, I guess genbox -ci option will not work to insert certain 
lipids if I already have a peptide in it. Looks like genbox -ci option only 
works for a single component system.
If you know how to use genbox to  insert certain lipid molecules in presence of 
peptide, please let me know.


From: Thomas Piggot <t.piggot at soton.ac.uk>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Tue, October 12, 2010 3:49:00 PM
Subject: Re: [gmx-users] How to incorporate WALP and KALP peptide in a Martini 

You can also self assemble the bilayer around your peptide. There is a 
tutorial on the Martini website for how to do this.



On 12/10/10 21:02, Justin A. Lemkul wrote:
> Sanku M wrote:
>> Hi,
>>    I am using MARTINI coarse-grained force-field to study interaction of
>> a transmembrane peptide WALP or KALP in a lipid-bilayer.  So,I  was
>> planning to insert a martini KALP or WALP peptide inside a martini DPPC
>> bilayer in a transmembrane manner. For that purpose, I was going through
>> the MARTINI JCTC paper( vol.4 , page-819 )  introducing the protein
>> force-field where a simulation study of KALP peptide in a bilayer has
>> been discussed ( in page 828 of that paper) .  But, I did not get any
>> details how the KALP or WALP peptide are inserted in a bilayer as
>> initial configuration.
>> So, I was wondering if I can get some help on how to insert this WALP
>> peptide in to Martini DPPC bilayer . I guess, there may be some way of
>> pulling , that may do the trick, but I am not sure how to keep it
>> trans-membrane as well during pulling . So, Any suggestions will be
>> helpful.
> In principle, building a CG membrane protein system and an atomistic one don't
> really differ, so you can follow the membrane protein tutorial.  You might 
> to modify the inflategro.pl script to recognize the atom naming for MARTINI
> lipids, though.
> http://www.gromacs.org/Documentation/Tutorials#Membrane_Simulations
> -Justin
>> Sanku
>> P.S:
>> I tried MARTINI coarse-grained simulation if the WALP peptide can get
>> spontaneously inserted in a 128-lipid DPPC bilayer( after starting from
>> a bulk water phase)  in a transmembrane manner . But, looks like it does
>> not get inserted in bilayer in a transmembrane manner, after 500 ns
>> simualtion. At the most, they remain in the interface of water
>> and lipids. I ran multiple configurations but in some cases it goes
>> other side of membrane. in some cases, it remained parallel in
>> interface.but never got inserted in a trans-membrane manner.

Dr Thomas Piggot
University of Southampton, UK.

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