Yeah I thought of steered molecular dynamics at first glance. But then I am
afraid because in that case, it will forcefully pull the peptide through
the lipid. So I will get the penetration behavior for non-penetrating
peptide as well. :-(
HM
On Fri, Jan 18, 2013 at 9:22 AM, Thomas Evangelidis <tevang3.gmail.com>wrote:
> Good question. I think you can deactivate the restraint when you see the
> peptide to enter the bilayer. Alternatively, in the flat-well restraint you
> define 4 cutoff distances (r1,r2,r3,4) (have a look in older threads). if
> the distance between the peptide and the lipid headgroup (R) is r2<R<r3
> then no force is applied. Thereby you can use values for those 2 cutoffs
> such that r3-r2>=[length of bilayer]. But I think the former solution would
> be better.
>
> Also you may want to consider steered MD, this is what people use in cases
> like yours.
>
> Thomas
>
>
> On 18 January 2013 10:10, HM <scienceamber.gmail.com> wrote:
>
> > 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
> > > >
> > > >
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
>
> ======================================================================
>
> Thomas Evangelidis
>
> PhD student
> University of Athens
> Faculty of Pharmacy
> Department of Pharmaceutical Chemistry
> Panepistimioupoli-Zografou
> 157 71 Athens
> GREECE
>
> email: tevang.pharm.uoa.gr
>
> tevang3.gmail.com
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Fri Jan 18 2013 - 01:00:02 PST
