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.
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 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. -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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