[gmx-users] How to incorporate WALP and KALP peptide in a Martini bilayer
Justin A. Lemkul
jalemkul at vt.edu
Wed Oct 13 00:21:07 CEST 2010
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.
> *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.
> 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.
> > -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
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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