As a quick follow-up question to this discussion (since the publication is
not yet out and I can't find this detail in the manual): does the new
lipid11 forcefield get things right without the need for constant surface
tension modifications? My understanding has been that at the moment only
the CHARMM36 forcefield can be used with lipids without this rather suspect
modification and still get the right densities, but I'm hoping that Lipid11
also has this property.
Thanks,
~Aron
On Tue, Apr 10, 2012 at 12:06 PM, Albert <mailmd2011.gmail.com> wrote:
> Thank you very much for kind update.
>
> If possible, would you please also specify how to insert out protein
> into pre-equilibrateed membrane by Amber. Since there many
> pre-equilibrated lipids are available but few comments on how to use
> them for our own system nowadays.
>
> My lab is going to buy a license for Amber 12 and I am looking forward
> to your tutorial.
>
> thanks again for kind reply.
>
> best
> Albert
>
>
> On 04/10/2012 05:58 PM, Benjamin D Madej wrote:
> > Hi Albert,
> >
> > Thanks for the question about membrane bound proteins. Amber 12 now
> includes the Lipid 11 modular phospholipid force field for lipids. You can
> check the manual for more details. We also have an upcoming paper about the
> force field.
> >
> > As for a membrane tutorial, I am working on writing one now, and it will
> be posted on the Amber web site.
> >
> > Ben Madej
> >
> > On Apr 10, 2012, at 5:52 AM, "Albert"<mailmd2011.gmail.com> wrote:
> >
> >> Dear:
> >>
> >> It is said that the Amber 12 has been improved a lot for membrane
> >> protein simulations in the maillist for quite a long time. However I
> >> don't find detailed information for this aspects, and I am wondering is
> >> there any tutorial for membrane protein simulations for Amber 12?
> >>
> >> thank you very much
> >> BET
> >> Albert
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>
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--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Tue Apr 10 2012 - 09:30:05 PDT
