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 vytvořena převratným poštovním 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 - 06:00:03 PDT
