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
On Fri, Jan 18, 2013 at 12:07 AM, Benjamin D Madej <bmadej.ucsd.edu> wrote:
> HM,
>
> 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. If you're simply trying to observe the peptide
> interacting with or crossing the bilayer, you'll probably need a large
> amount of sampling in hopes of seeing a peptide-bilayer interaction. With
> periodic boundaries, the peptide will (eventually) interact with the
> bilayer.
>
> But the questions are: Why is this a control? What are you measuring or
> investigating in this study? Is this really an appropriate method/approach?
> It's not clear what your methodology is.
>
> Ben Madej
> Walker Molecular Dynamics Lab
> ________________________________________
> From: HM [scienceamber.gmail.com]
> Sent: Thursday, January 17, 2013 2:28 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Membrane-Peptide Simulation ( peptide going away from
> membrane)
>
> Dear Ben,
> Thank you for your reply. Here I am giving detail of my system:
> Peptide: 10 amino acid long ( known to interact and penetrate across the
> membrane)
> Lipid molecules: 274 (bilayer)
> lipid type: POPC, forcefield : gaff
> AMBER version: Amber10 sander
>
> Behaviour expectation: I expect during my simulation the peptide should
> cross the membrane
>
> Thanks and Regards,
> HM
>
>
>
> On Tue, Jan 15, 2013 at 6:49 PM, Benjamin D Madej <bmadej.ucsd.edu> wrote:
>
> > HM,
> >
> > It's not clear what your approach is for this simulation. How exactly is
> > your system set up (i.e. system size, number of lipid bilayers, number of
> > waters, number of peptides)? What is the peptide and the mechanism of
> > transport across the membrane? Can you clarify what behavior you expected
> > from this simulation?
> >
> > In addition, there's already been some work done in our group and our
> > collaborators for lipid parameter sets for Amber. Take a look at the
> > parameter sets Lipid11 and GAFFlipid (Skjevik et al, J. Phys. Chem. B,
> > 2012; Dickson et al, Soft Matter, 2012).
> >
> > Ben Madej
> > Walker Molecular Dynamics Lab
> >
> > On Jan 15, 2013, at 9:18 AM, HM <scienceamber.gmail.com> wrote:
> >
> > > Hi All,
> > > In my study, I am trying to see the membrane penetrating behavior of
> few
> > > peptides. As a control, I took the peptide which is well known to cross
> > the
> > > membrane. I prepared the peptide structure (20 amino acid long ) and 20
> > ns
> > > simulation to get the stable conformation. Now I prepared the membrane
> > > (POPC) and kept the peptide over the membrane (using VMD). I generated
> > the
> > > lipid parameters using AM1-BCC method and then performed the simulation
> > > (minimization, heating, equilibration.)
> > >
> > > Now during simulation the peptide goes away ( within ns) from the
> lipid
> > > membrane and it never comes back ( during simulation of 20ns).
> > >
> > > I guess there is no point of continuing the simulation ? Can you please
> > > help me to get rid of this issue.
> > >
> > > Thanks,
> > > HM
> > > _______________________________________________
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> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
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> >
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Received on Fri Jan 18 2013 - 00:00:03 PST
