[gmx-users] pH dependent simulation

zaved at tezu.ernet.in zaved at tezu.ernet.in
Mon Nov 27 06:24:15 CET 2017

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

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