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/
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>
--
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
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Received on Thu Nov 14 2013 - 12:00:03 PST
