Thanks Thomas for your reply.
Just one quick query. If I will keep the flat-well restrain on peptide
close to lipid head group. Then I expect that there will be no moving away
phenomenon but at the same time is it not true that it will also not go
inside the membrane due to restrain w.r.t. lipid head group ?
Thanks,
HM
On Fri, Jan 18, 2013 at 8:52 AM, Thomas Evangelidis <tevang3.gmail.com>wrote:
> You can apply a flat-well restraint that will keep the peptide close to a
> lipid head group and then just pray for your peptide to pass through the
> bilayer. I would certainly use an enhanced sampling algorithm to monitor
> this phenomenon, but as far as I know membranes are peculiar systems and
> the conventional aMD algorithm implemented in AMBER is not suitable for
> that type of simulation. I would search the literature to see what other
> people have used for similar cases.
>
> Thomas
>
>
> On 18 January 2013 09:29, HM <scienceamber.gmail.com> wrote:
>
> > Hi Ben,
> >
> > *"You placed the peptide next to the lipid bilayer with VMD. It sounds
> like
> > you expect the peptide insert into the membrane and cross the bilayer,
> but
> > it diffused away. "*
> > Yes this is what exactly I did, I expect and I am getting. :-(
> >
> > *"you'll probably need a large amount of sampling in hopes of seeing a
> > peptide-bilayer interaction. "*
> > If I understand you correctly, Shall I continue previous simulation and
> > hope for peptide-bilayer interaction
> >
> > *Why is this a control? What are you measuring or investigating in this
> > study?*
> > This is control because It is already proven (in several experiments)
> that
> > given peptide interacts with membrane and finally crosses it. And I want
> to
> > keep it as control because I have bunch of peptides in my hand, for
> which I
> > am interested in testing their membrane crossing behavior. The one which
> > will give positive result, I will use further for my lab work.
> >
> > *Is this really an appropriate method/approach? *
> > I don't know whether it is an appropriate approach or not. I thought
> about
> > it and trying to perform the simulations. If you can correct me or
> suggest
> > something then please do it. Just for your info, I have amber10 and
> amber11
> > and not amber12 at my system. So for all my work, I can use only both of
> > them and not Amber12 (which recently added membrane force-fields with
> nice
> > tutorial).
> >
> > Thanks,
> > HM
> >
> >
> >
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Received on Fri Jan 18 2013 - 00:30:02 PST
