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/
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jan 18 2013 - 00:30:03 PST
