On Tue, Jan 31, 2012 at 8:08 AM, George Tzotzos <gtzotzos.me.com> wrote:
> Thanks Jason,
>
> The "lid" is kept in position NOT by the terminal carboxylate but by
> adjacent residues forming Hbonds. The terminal carboxylate does not form
> Hbonds.
>
But does it protonate in the pH range that you're going to be titrating?
If the carboxylate's protonation state is important, then sander will not
be able to model that for you. If it's unimportant, then sander should
work fine.
The problem is not the existing code, but rather no C-terminal residues (or
N-terminal residues) have been parametrized to work with the constant pH
method, although the workflow for treating them is well-defined.
HTH,
Jason
> George
>
>
> On Jan 31, 2012, at 2:00 PM, Jason Swails wrote:
>
> > Sander cannot currently titrate termini, although that's on the list of
> things to do (at some point).
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> >
> > On Jan 31, 2012, at 7:26 AM, George Tzotzos <gtzotzos.me.com> wrote:
> >
> >> Hi everybody,
> >>
> >> I'm dealing with a protein in which the C-terminal end forms a lid over
> the binding site. I has been proposed that this lid is acid labile and that
> at low pH it "uncovers" the binding pocket thus releasing the bound ligand.
> >>
> >> My question is whether the constant pH in method in combination with
> conventional MD as implemented in Sander is appropriate to study whether
> this hypothesis is right?
> >>
> >> I'm asking this before going into a wild goose chase. Any suggestions
> will be most welcome.
> >>
> >> Many thanks in advance for any advice.
> >>
> >> George
> >>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Jan 31 2012 - 07:30:02 PST
