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 - 00:00:04 PST
