[gmx-users] pH dependent simulation

Tasneem Kausar tasneemkausar12 at gmail.com
Mon Nov 27 07:02:10 CET 2017

pKa of amino acid residue is a constant quantity. Depending on the pH you
can protonate and deprotonate amino acid according to the pKa of particular


On Mon, Nov 27, 2017 at 9:39 AM, <zaved at tezu.ernet.in> wrote:

> Hello Everyone
> I am trying to simulate a protein at two pH (7.4 and 9.0) using
> gromacs 5.1.4. The protein has no missing residues. Optimal pH range is
> 6.0 to 9.0 and pI of the protein is 11.4. It has 9 negatively and 17
> positively charged residues.
> However upon predicting the pKa values using H++ server, I am getting the
> same pKa values for all the charged residues (at pH 7.4 and pH 9). And the
> total charge of +8e is also same at both pH 7.4 and 9.0. (Instead it
> should have different pKa values at pH 7 and 9).
> Whether I am in the right direction or doing something wrong!!!
> Can anyone kindly suggest me how to proceed further?
> Any suggestion is appreciated.
> Thank You
> Zaved
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