Hi,
calckpka read the output of constant pH MD, therefore is not useful in my
case. Is there any other third party tool I could use to find the
protonation of the binding pocket at a given pH value?
thanks,
Thomas
On 14 November 2013 21:50, Dwight McGee <dwight.mcgee.gmail.com> wrote:
> Hi,
>
> I would take a look at the constant pH MD tutorial (
> http://ambermd.org/tutorials/advanced/tutorial18/). The program
> *calckpka* is
> used to analyze the results from constant pH MD simulations.
>
>
> On Thu, Nov 14, 2013 at 2:30 PM, Thomas Evangelidis <tevang3.gmail.com
> >wrote:
>
> > Dear AMBER community,
> >
> > I am simulating a protein-complex in which protonation of two glutamic
> > acids in the binding pocket is believed to dictate ligand binding and
> > release. I want to calculate pKa values from conformations along the
> > simulation and change if necessary the protonation of the protein by also
> > taking into account the ligand. I used for this purpose PROPKA 3.1 and
> H++
> > servers, but the results are contradictory. According to PROPKA 3.1 the
> pKa
> > values of the two Glu residues in the starting conformation are 8.07 and
> > 7.61, therefore in pH 7.6 both will be protonated. According to the
> > titration curves produced by H++ these two residues are never protonated
> at
> > pH 7.6 whatever dielectric I use for the protein (tried values 1-10). It
> is
> > worth noting that the titration curve of the first Glu deviates a lot
> from
> > the Henderson-Hasselbalch curve.
> >
> > I am confused about what results I should trust. Is there a program in
> > AmberTools to calculate pKa values and protonate by taking into account
> the
> > effect of the ligand? I found in the manual a program named calcpka but I
> > cannot understand the arguments it takes. Is there any other tool that
> you
> > would recommend for that purpose?
> >
> > thanks in advance,
> > Thomas
> >
> >
> >
> > --
> >
> > ======================================================================
> >
> > Thomas Evangelidis
> >
> > PhD student
> > University of Athens
> > Faculty of Pharmacy
> > Department of Pharmaceutical Chemistry
> > Panepistimioupoli-Zografou
> > 157 71 Athens
> > GREECE
> >
> > email: tevang.pharm.uoa.gr
> >
> > tevang3.gmail.com
> >
> >
> > website: https://sites.google.com/site/thomasevangelidishomepage/
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> T. Dwight McGee Jr.
> Quantum Theory Project
> University of Florida
> Graduate Student
> dwight.mcgee.gmail.com
>
> "Problems cannot be solved at the same level of awareness that created
> them."
> Albert Einstein
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang.pharm.uoa.gr
tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Thu Nov 14 2013 - 12:30:03 PST
