Thank you for your reply.
But, I am following this tutorial.
https://pmc.ncbi.nlm.nih.gov/articles/PMC9910290/
The define two tautomeric states as
if i == 1:
if x[0] >= up_cut and x[1] >= up_cut:
x1_count += 1
if x[0] >= up_cut and x[1] <= low_cut:
x2_count += 1
*i=1 means histidine*
*Then I calculate a fraction of x1_counts and x2_counts with different pH.*
But I get a high pka value for x1_counts compared to others. But from
experimental result we know that pka for HIP to HID is 7.0 and HIP to HIE
is 6.5
On Wed, Sep 3, 2025 at 10:09 PM Adrian Roitberg <roitberg.ufl.edu> wrote:
>
> On 9/3/25 11:15 AM, Dulal Mondal wrote:
>
> *[External Email]*
> Thank you for your reply.
> Yes.
> But my question is which is correct?
> x =1 (HID) and x=0 (HIE)
> x=0 (HID) and x=1 (HIE)
>
>
>
> x=0, lambda=1 for HID
> x=1, lambda=1 for HIE
>
>
>
> On Wed, Sep 3, 2025 at 8:33 PM Adrian Roitberg <roitberg.ufl.edu> wrote:
>
>> Hi Dulal
>>
>> Do you understand the difference between HID and HIE, outside the scope
>> of constant pH ?
>>
>> Adrian
>>
>>
>> On 9/3/25 10:58 AM, Dulal Mondal via AMBER wrote:
>> > [External Email]
>> >
>> > Dear Experts,
>> >
>> > I am trying continuous constant pH (chapter 26) of amber24. I can not
>> > understand the definition of HIS residue. For this, two variables are
>> > needed (lambda and x).
>> >
>> > If lambda =0 means protonated (HIP), if lambda =1 deprotonated
>> (HID/HIE).
>> >
>> > But for the x.
>> >
>> > if x =1 (HID) and x=0 (HIE).
>> >
>> > I can not understand the x definition. Please provide me with the
>> correct
>> > definition of lambda and x for this.
>> >
>> > --
>> > *With regards,*
>> > *Dulal Mondal,*
>> > *Research Scholar,*
>> > *Department of Chemistry,*
>> > *IIT Kharagpur, Kharagpur 721302.*
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>> --
>> Dr. Adrian E. Roitberg
>> Frank E. Harris Professor
>> Department of Chemistry
>> University of Florida
>> roitberg.ufl.edu
>> 352-392-6972
>>
>>
>
> --
> *With regards,*
> *Dulal Mondal,*
> *Research Scholar,*
> *Department of Chemistry,*
> *IIT Kharagpur, Kharagpur 721302.*
>
> --
> Dr. Adrian E. Roitberg
> Frank E. Harris Professor
> Department of Chemistry
> University of Floridaroitberg.ufl.edu
> 352-392-6972
>
>
--
*With regards,*
*Dulal Mondal,*
*Research Scholar,*
*Department of Chemistry,*
*IIT Kharagpur, Kharagpur 721302.*
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Received on Wed Sep 03 2025 - 10:30:02 PDT
