[gmx-users] Protein at given pH

[Steven Neumann]

On Wed, Nov 7, 2012 at 2:55 PM, Erik Marklund <erikm at xray.bmc.uu.se> wrote:
> Hi,
>
> I've used the H++ server myself at times. My experience is that it's rather sensitive to the very fine detail of the input structure in some cases. I've had situations where H++ suggest one protonation state, then a short md simulation takes the system to a slightly different conformation that seem more prevalent but that yields another protonation state if sent to H++ again. Use all biochemical knowledge that you can muster to check that the output makes sense. Focus on residues that you suspect might be important for the overall question you address.
>
> That said, pKa calculations are inherently difficult and can probably not be done reliably without lots of simulations. As such H++ probably come close to what we can currently accomplish within reasonable time for (nearly) static structures.
>
> Best,
>
> Erik

Thanks for this! Is it not better just to use pK values from the
literature corresponding to given residue side chain? My protein is an
alpha-helix.

Thanks,

Steven


>
> 7 nov 2012 kl. 10.19 skrev Steven Neumann:
>
>> Dear Gmx Users,
>>
>> I am trying to simulate protein-ligand interactions at specific pH=5.
>> I processed my protein.pdb into the H++. As I see from th titration
>> curve of the entire molecule it appears that at pH=5 the total charge
>> should be equal to 2. When I process the obtained pdb from the server
>> to pdb2gmx using -ignh I get the total charge of -3. Can anyone
>> explain me this?
>>
>> In terms of small molecules how can I get parameters at specific pH? I
>> am using Charmm and parachem.org does not support pH changes. Can
>> anyone advise?
>>
>> thank you,
>>
>> Steven
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> -----------------------------------------------
> Erik Marklund, PhD
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,    75124 Uppsala, Sweden
> phone:    +46 18 471 6688        fax: +46 18 511 755
> erikm at xray.bmc.uu.se
> http://www2.icm.uu.se/molbio/elflab/index.html
>
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