[gmx-users] pH dependent simulation

Justin Lemkul jalemkul at vt.edu
Mon Nov 27 14:32:59 CET 2017



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.
>
> <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail>
> Virus-free.
> www.avast.com
> <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail>
> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>
> 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
>>
>>
>> * * * D I S C L A I M E R * * *
>> This e-mail may contain privileged information and is intended solely for
>> the individual named. If you are not the named addressee you should not
>> disseminate, distribute or copy this e-mail. Please notify the sender
>> immediately by e-mail if you have received this e-mail in error and destroy
>> it from your system. Though considerable effort has been made to deliver
>> error free e-mail messages but it can not be guaranteed to be secure or
>> error-free as information could be intercepted, corrupted, lost, destroyed,
>> delayed, or may contain viruses. The recipient must verify the integrity of
>> this e-mail message.
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>

-- 
==================================================

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
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================



More information about the gromacs.org_gmx-users mailing list