[gmx-users] Protein at given pH

[Tsjerk Wassenaar]

Hi,

Do you mean the pKa value of the side chain in solution? Or the pKa value
in ethanol, DMSO, hexane? Maybe the pKa value in a membrane, or in the
interior of a protein, perhaps in a hydrophobic pocket? Or the pKa with
one/two/three neighbouring acidic/basic residues? If you have literature
values applying to your case, sure, go ahead and use them!

Cheers,

Tsjerk


On Wed, Nov 7, 2012 at 4:21 PM, Steven Neumann <s.neumann08 at gmail.com>wrote:

> 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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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
Canada