Dear Alexey,
thank you very much for your complete answer !
Best wishes,
Marek
Dne Tue, 27 Apr 2010 14:43:17 +0200 Ramu Anandakrishnan <ramu.vt.edu>
napsal/-a:
> Forwarding message from Dr. Alexey Onufriev.
>
> --------------------------------------------------
> From: <alexey.vt.edu>
> Sent: Monday, April 26, 2010 6:30 PM
> To: <amber.ambermd.org>
> Cc: <ramu.cs.vt.edu>
> Subject: Fwd: Fw: Fw: [AMBER] The resonable way how to protonate protein
> for Amber simulation in explicit water ?
>
>> Hi, Marek.
>>
>> Depending on how much effort you are willing to spend here are a few
>> options for
>> you,
>> starting from the least time consuming.
>>
>>
>> 1. Just run your PDB structure through H++ webserver
>> (biophysics.cs.vt.edu/H++
>> ). Use default input
>> parameters and set the pH you need. Don't forget to check the AMBER
>> explicit solvent box.
>> This will set up your structure in the protonation state appropriate
>> for the
>> given pH. You will
>> get both the PDB and AMBER prmtop and inpcrd files.
>>
>> 2. First, finesse your PDB through MolProbity server
>> (molprobity.biochem.duke.edu), then go to step 1 above.
>>
>>
>> 3. Start with step 2, but then run the structure resulting from H++
>> through
>> MolProbity again, to see if it suggests
>> alternate positions for any of the protons on HIS. In H++,
>> deprotonated HIS
>> defaults to HIE (HIS-epsilon), which is AMBER convention, but
>> obviously not
>> always right.
>>
>>
>> To answer your second question: yes, at the moment you have to use fixed
>> protonation states in "standard" explicit solvent MD,
>> so the best you can do is to try to set them up correctly at the start.
>> Of
>> course, if any of the states are available experimentally,
>> use those.
>>
>>
>> Keep the default value of internal epsilon in H++, unless you really
>> know what
>> you are doing. H++ pK calculations are based on
>> the single conformer continuum solvent model where epsilon_in > 1 is
>> appropriate.
>>
>>
>>
>> regards, Alexey Onufriev
>>
>> Ramu Anandakrishnan
>>
>>
>>>>> --------------------------------------------------
>>>>> From: "Marek Maly" <marek.maly.ujep.cz>
>>>>> Sent: Tuesday, April 20, 2010 3:54 PM
>>>>> To: <amber.ambermd.org>
>>>>> Subject: [AMBER] The resonable way how to protonate protein for Amber
>>>>> simulation in explicit water ?
>>>>>
>>>>>> 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 ?
>>>>>>
>>>>>> If yes, what is the recommended procedure for protein protonation
>>>>>> respect to given pH ?
>>>>>>
>>>>>> 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 ?
>>>>>>
>>>>>> 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 ?
>>>>>>
>>>>>> Thanks a lot in advance for any valuable comments/experiences !
>>>>>>
>>>>>> Best wishes,
>>>>>>
>>>>>> Marek
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Tato zpráva byla vytvoøena pøevratným po¹tovním klientem Opery:
>>>>>> http://www.opera.com/mail/
>>>>>>
>>>>>> _______________________________________________
>>>>>> AMBER mailing list
>>>>>> AMBER.ambermd.org
>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>>>
>>
>> ----- End forwarded message -----
>>
>>
>>
>
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Received on Tue Apr 27 2010 - 08:00:03 PDT
