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

[Justin A. Lemkul]

Sanku M wrote:
> 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.
> 

You could probably save yourself quite a bit of time by going ahead and trying 
to use genbox -ci.  You can definitely insert lipid molecules into a box that 
contains some other species, provided that there is sufficient space in the box 
for the molecules you're inserting.

-Justin

> Sanku 
> 
> 
> ------------------------------------------------------------------------
> *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 bilayer
> 
> You can also self assemble the bilayer around your peptide. There is a
> tutorial on the Martini website for how to do this.
> 
> Cheers
> 
> Tom
> 
> 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 have
>  > to modify the inflategro.pl <http://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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-- 
========================================

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

========================================