[gmx-users] pH dependent simulation

[Tasneem Kausar]

Thanks for correcting......

On Mon, Nov 27, 2017 at 7:02 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/27/17 1:02 AM, Tasneem Kausar wrote:
>
>> pKa of amino acid residue is a constant quantity. Depending on the pH you
>>
>
> That's not strictly true. Titratable amino acids can be found in unique
> microenvironments that cause shifts in canonical values. For instance,
> there are some catalytic lysines known in hydrophobic environments that
> have pKa values of ~4 instead of the canonical value of ~10.5.
>
> -Justin
>
> can protonate and deprotonate amino acid according to the pKa of particular
>> residue.
>>
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>> 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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