Dear Jason,
thanks again for your additional info !
Best wishes,
Marek
Dne Wed, 21 Apr 2010 22:02:10 +0200 Jason Swails <jason.swails.gmail.com>
napsal/-a:
> 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
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>> __________ Informace od ESET NOD32 Antivirus, verze databaze 5036
>>> (20100417) __________
>>>
>>> Tuto zpravu proveril ESET NOD32 Antivirus.
>>>
>>> http://www.eset.cz
>>>
>>>
>>>
>>>
>>
>> --
>> Tato zpráva byla vytvořena převratným poštovním klientem Opery:
>> http://www.opera.com/mail/
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
--
Tato zpráva byla vytvořena převratným poštovním klientem Opery:
http://www.opera.com/mail/
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Apr 21 2010 - 16:30:04 PDT
