Not that is commonly used with AMBER apparently.
Why not just run simulations of all 4 protonation states (if running
constant pH is too much trouble)? That seems more defensible then just
making up a protonation state based off some unrelated program.
Regards,
Brian
On Thu, Nov 14, 2013 at 3:14 PM, Thomas Evangelidis <tevang3.gmail.com>wrote:
> 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
> > AMBER.ambermd.org
> > 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/
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Thu Nov 14 2013 - 12:30:04 PST
