You can also run constant pH MD to obtain pKas, and based on your
results set your protonation state for explicit water MD, etc. pKas
are inherently ensemble-averaged properties, so no *single* structure
can give you a reliable pKa for a buried ionizable residue.
Note that constant protonation is NOT constant pH, as Carlos pointed
out. It can be a good approximation if one protonation state is
vastly dominant over the other, but there will always exist members of
the ensemble with a different protonation state. For that reason, it
may be useful to run constant pH MD to see if the constant-protonation
state choice you were going to make is valid.
All the best,
Jason
On Fri, Apr 16, 2010 at 12:53 PM, Dean Cuebas
<deancuebas.missouristate.edu> wrote:
>
> Dear Andrew,
>
> I have found the best approach to protonating my proteins is to use the pKa
> predictions of the H++ server in conjunction with the superior H-bonding
> prediction of reduce at the Molprobity server.
>
> 1) Use Molprobity to flip Asn, Gln, His residues as needed, since MOST
> proteins from XRC need fixing in this regard.
> 2) Save the flipped but NOT protonated pdb to use as input to the H++ server
> for pKa predictions.
> 3) Continue with the Molprobity server to maximize H-bonding possibilities
> and protonate the protein.
>
> 4) Using visual inspection of the molprobity output for h-bond and clashes,
> and the pKa predictions of H++ you can come to some reasonably confident
> expectations, especially with regards to the correct state of histidine,
> picking the correct HID or HIE neutral annular tautomer, or the protonated
> HIP.
>
> Realize that constant pH cannot be used with explicit water MD, so if you
> use a water box, you should do the above.
>
> Hope this helps!
>
> Dean
>
>
>> From: Carlos Simmerling <carlos.simmerling.gmail.com>
>> Reply-To: AMBER Mailing List <amber.ambermd.org>
>> Date: Fri, 16 Apr 2010 11:10:42 -0500
>> To: AMBER Mailing List <amber.ambermd.org>
>> Subject: Re: [AMBER] how is pH treated in Amber - other than constant pH
>> simulations
>>
>> simulations in amber are either constant pH or constant protonation.
>> default protonations are reasonable for the isolated amino acids, but
>> pka shifts may occur in proteins. it is possible to calculate pkas for
>> the initial structure, assign protonation states, and keep them. this
>> is ok as long as there are not conformation dependent pka changes that
>> cross your pH.
>>
>> On 4/16/10, Andrew Voronkov <drugdesign.yandex.ru> wrote:
>>> Dear Amber users,
>>> when I am looking for questions about pH and Amber I get mostly information
>>> about constant pH simulations. But what pH is supposed to be by default,
>>> without constant pH simulations? Just neutral or what it depends from?
>>> As I understand in Amber pH is mostly set by protonation state of the
>>> molecules, so if not going to constant pH simulation I can approximately
>>> imitate some pH by setting corresponding protonation state distribution of
>>> amino acids. If physiological pH is required for protein simulation what can
>>> be general recommendation here - instant pH or default pH treatment?
>>>
>>> Sincerely yours,
>>> Andrew
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>> --
>> ===================================================================
>> Carlos L. Simmerling, Ph.D.
>> Professor, Department of Chemistry
>> CMM Bldg, Room G80 Phone: (631) 632-1336 Fax: 632-1555
>> Stony Brook University E-mail: carlos.simmerling.gmail.com
>> Stony Brook, NY 11794-5115 Web: http://www.simmerlinglab.org
>> ===================================================================
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Fri Apr 16 2010 - 11:30:04 PDT
