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 <[email protected]>
*To:* Discussion list for GROMACS users <[email protected]>
*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
========================================
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