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
> > _______________________________________________
> > 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jan 17 2013 - 03:00:02 PST
