[gmx-users] pH dependent simulation

Justin Lemkul jalemkul at vt.edu
Mon Nov 27 14:31:31 CET 2017

On 11/26/17 11:09 PM, 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).

Why do you expect that? There are no amino acids with pKa in that range, 
so nothing should change unless there are unique microenvironments that 
shift canonical pKa values. As H++ has not detected any, likely your 
protein behaves canonically. You can confirm your calculated pKa values 
with another method, like PROPKA, to be sure.


> 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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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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