<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:'times new roman', 'new york', times, serif;font-size:12pt"><div>Hi Tom,</div><div> 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.</div><div>If you know how to use genbox to insert certain lipid molecules in presence of peptide, please let me know.</div><div><br></div><div>Sanku </div><div><br></div><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><br><div style="font-family:arial, helvetica, sans-serif;font-size:13px"><font
size="2" face="Tahoma"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Thomas Piggot <t.piggot@soton.ac.uk><br><b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Tue, October 12, 2010 3:49:00 PM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] How to incorporate WALP and KALP peptide in a Martini bilayer<br></font><br>
You can also self assemble the bilayer around your peptide. There is a <br>tutorial on the Martini website for how to do this.<br><br>Cheers<br><br>Tom<br><br>On 12/10/10 21:02, Justin A. Lemkul wrote:<br>><br>> Sanku M wrote:<br>> <br>>> Hi,<br>>> I am using MARTINI coarse-grained force-field to study interaction of<br>>> a transmembrane peptide WALP or KALP in a lipid-bilayer. So,I was<br>>> planning to insert a martini KALP or WALP peptide inside a martini DPPC<br>>> bilayer in a transmembrane manner. For that purpose, I was going through<br>>> the MARTINI JCTC paper( vol.4 , page-819 ) introducing the protein<br>>> force-field where a simulation study of KALP peptide in a bilayer has<br>>> been discussed ( in page 828 of that paper) . But, I did not get any<br>>> details how the KALP or WALP peptide are inserted in a bilayer as<br>>>
initial configuration.<br>>> So, I was wondering if I can get some help on how to insert this WALP<br>>> peptide in to Martini DPPC bilayer . I guess, there may be some way of<br>>> pulling , that may do the trick, but I am not sure how to keep it<br>>> trans-membrane as well during pulling . So, Any suggestions will be<br>>> helpful.<br>>><br>>> <br>> In principle, building a CG membrane protein system and an atomistic one don't<br>> really differ, so you can follow the membrane protein tutorial. You might have<br>> to modify the <a target="_blank" href="http://inflategro.pl">inflategro.pl</a> script to recognize the atom naming for MARTINI<br>> lipids, though.<br>><br><span>> <a target="_blank" href="http://www.gromacs.org/Documentation/Tutorials#Membrane_Simulations">http://www.gromacs.org/Documentation/Tutorials#Membrane_Simulations</a></span><br>><br>>
-Justin<br>><br>> <br>>> Sanku<br>>><br>>><br>>> P.S:<br>>><br>>> I tried MARTINI coarse-grained simulation if the WALP peptide can get<br>>> spontaneously inserted in a 128-lipid DPPC bilayer( after starting from<br>>> a bulk water phase) in a transmembrane manner . But, looks like it does<br>>> not get inserted in bilayer in a transmembrane manner, after 500 ns<br>>> simualtion. At the most, they remain in the interface of water<br>>> and lipids. I ran multiple configurations but in some cases it goes<br>>> other side of membrane. in some cases, it remained parallel in<br>>> interface.but never got inserted in a trans-membrane manner.<br>>><br>>><br>>> <br>> <br><br>-- <br>Dr Thomas Piggot<br>University of Southampton, UK.<br><br>-- <br>gmx-users mailing list <a
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