[gmx-users] pH dependent simulation
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
> * * * D I S C L A I M E R * * *
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Justin A. Lemkul, Ph.D.
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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