Re: [AMBER] protonation of protein-ligand complex

From: Adrian Roitberg <>
Date: Thu, 14 Nov 2013 16:22:51 -0500

Dear Thomas,

One minor correction to your email. If truly the pKas are 8.07 and 7.6,
then you CANNOT assume that at pH 7.6 they will be both protonated! In
fact, this is the nightmare scenario, where the pH and pKa are very
close to each other. This means that you are very close to 50/50%
protonated/deprotonated and any particular choice of protonation states
is by definition, wrong.


On 11/14/13 2:30 PM, Thomas Evangelidis 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

                             Dr. Adrian E. Roitberg
Colonel Allan R. and Margaret G. Crow Term Professor.
Quantum Theory Project, Department of Chemistry
University of Florida
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Received on Thu Nov 14 2013 - 13:30:03 PST
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