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.
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.
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