Hello,
2010/4/21 Marek Maly <marek.maly.ujep.cz>
> Dear Jason,
>
> thanks a lot for your comments !
>
> Regarding to H++ sw I thaught that it is well known and used in Amber
> community since it is
> one of the useful SW listed on Amber page (please see "Related software
> that interfaces with Amber").
> The direct link is: http://biophysics.cs.vt.edu/H++/
>
> I think that physics background for H++ and "Amber MD under constant pH"
> regarding
> to protonation is probably the same or very similar.
>
> I think that compatibility of internal dielectric constant in H++ and Amber
> if one
> uses H++ for protonation is important question and would be nice to have
> satisfactory answer.
>
> Intuitively it seems that changing internal dielec. in H++ from default 6
> to 1
> is resonable but I am not sure about since maybe there could be some small
> differences
> in algorithms and the result obtained in H++ with internal diel. constant 6
> regarding to
> protonation states might be the same like results obtained for example
> during Amber MD under constant
> pH with internal diel. 1 (again just regarding to protonation).
>
> Of course that this could be answered (at least regarding concrete
> molecule) with several trials.
>
> OK, I have last question.
>
> Regarding to MD under constant pH in Amber, which molecules are
> automatically protonated here
> according to given pH and actual conformation. Only proteins ?
>
Currently, only ASP, GLU, HIS, LYS, and TYR residues are parametrized for
titration. However, reading Mongan's paper (referenced in the Amber manual)
and following the instructions there and in the manual will help you
parametrize more residues if you so desire.
Good luck!
Jason
>
> Thanks again !
>
> Best,
>
> Marek
>
>
>
>
>
>
>
> Dne Wed, 21 Apr 2010 15:35:38 +0200 Jason Swails <jason.swails.gmail.com>
> napsal/-a:
>
> Hello,
>>
>> 2010/4/20 Marek Maly <marek.maly.ujep.cz>
>>
>> Dear all,
>>>
>>> just a quick technical question. I am just wondering
>>> what is the recommended way of preparing protein structure
>>> for simulation in explicit water under given pH.
>>>
>>> If I am not wrong, in this case simulation under constant pH
>>> has to be approximated by simulation with fixed "correspondent"
>>> protonation state of the given protein. Am I right ?
>>>
>>>
>> Yes. Explicit MD is not yet supported under constant pH MD, so you will
>> have to choose a constant protonation state.
>>
>>
>> If yes, what is the recommended procedure for protein protonation
>>> respect to given pH ?
>>>
>>>
>> I think it really depends on the system. If you're simulating a
>> solvent-exposed carboxylate at pH 7, this is really a no-brainer for the
>> most part. If you're looking at a buried residue or something with a pKa
>> relatively close to the pH, it's a more complicated issue.
>>
>>
>>
>>> It is for example sufficient to use just H++ server to assign protonation
>>> states
>>> to all ionisable groups regarding to given pH and of course regarding to
>>> the given
>>> (representative) protein conformation ?
>>>
>>>
>> This seems reasonable to me. However, like you mentioned, this will not
>> take into account (as far as I know), conformational-dependent pKa shifts.
>> Another option, of course, is to run constant pH MD using sander and take
>> the protonation states dominant throughout that simulation for your
>> explicit
>> simulation. This approach would be more "correct", though it certainly
>> takes a little bit longer to decide on protonation states (though it's
>> probably the best approach for complex systems.
>>
>>
>>
>>> Speaking about H++ it is OK to keep their default value of internal
>>> protein
>>> dielectric constant which has the
>>> value 6 or one have to change it to value 1 which is the only recommended
>>> value in any Amber implicit solvent
>>> calculation including MM/PBSA which I would like to carry out with my
>>> protein/X complex after explicit water MD ?
>>>
>>>
>> I don't know anything about this software, so I can't comment here.
>>
>>
>>
>>> Thanks a lot in advance for any valuable comments/experiences !
>>>
>>> Best wishes,
>>>
>>> Marek
>>>
>>>
>> Good luck!
>> Jason
>>
>> ---------------------------------------
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Graduate Student
>> 352-392-4032
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>
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--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Apr 21 2010 - 13:30:05 PDT
