Hello Jason
Thanks for your explanations!
I am running Sander for protein/water/ions simulation. The protein
should carry charge although the whole system is neutralized by adding
the counter ions.
So according to you, in amber, except the manually adjusting protonation
state,
the only way is to run the constant pH molecular first to obtain the correct
state of each residue and then switch to normal MD simulation in Sander.
Can I play this trick to save some time?
Thanks,
Tom
On Wed, Jan 27, 2010 at 3:31 PM, Jason Swails <jason.swails.gmail.com>wrote:
> Hello,
>
> On Wed, Jan 27, 2010 at 6:11 PM, Tom Williams <dnaafm.gmail.com> wrote:
> > Dear Ross,
> >
> > Thanks for your quick response to clarify this question!
> >
> > Could you give me one more suggestion?
> > Does Amber provide any tool or command that can deprotonate / protonate a
> > protein
> > or peptide at certain pH ?
>
> This is a tricky question... You can run constant pH molecular
> dynamics in which the protonation state of each "titratable" residue
> is changed according to a monte carlo criteria. Alternatively,
> different protonated states of residues have different names (for
> instance, ASP is an aspartate deprotonated, and ASH is an aspartic
> acid with a proton, same for GLU and GLH). You would have to decide
> whether you want to run constant pH simulations (this is described in
> the manual), or whether you want to set the protonation states of each
> of the acid/base groups. However, there's no way to set the pH and
> have a program *figure out* what the appropriate protonation state
> would be -- you'd actually have to run the constant pH MD.
>
> Hope this helps,
> Jason
>
> --
> ---------------------------------------
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
>
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Received on Thu Jan 28 2010 - 17:00:02 PST
