Btw, why do you suggest to use not protonated structure from MolProbity first? Well at least for my pretty simple protein the H++ predictions, based on protonated and non-protonated models from MolProbity look pretty the same, so why not to use protonated one?
Best regards,
Andrew
16.04.10, 11:53, "Dean Cuebas" <deancuebas.missouristate.edu>:
>
> Dear Andrew,
>
> I have found the best approach to protonating my proteins is to use the pKa
> predictions of the H++ server in conjunction with the superior H-bonding
> prediction of reduce at the Molprobity server.
>
> 1) Use Molprobity to flip Asn, Gln, His residues as needed, since MOST
> proteins from XRC need fixing in this regard.
> 2) Save the flipped but NOT protonated pdb to use as input to the H++ server
> for pKa predictions.
> 3) Continue with the Molprobity server to maximize H-bonding possibilities
> and protonate the protein.
>
> 4) Using visual inspection of the molprobity output for h-bond and clashes,
> and the pKa predictions of H++ you can come to some reasonably confident
> expectations, especially with regards to the correct state of histidine,
> picking the correct HID or HIE neutral annular tautomer, or the protonated
> HIP.
>
> Realize that constant pH cannot be used with explicit water MD, so if you
> use a water box, you should do the above.
>
> Hope this helps!
>
> Dean
>
>
> > From: Carlos Simmerling
> > Reply-To: AMBER Mailing List
> > Date: Fri, 16 Apr 2010 11:10:42 -0500
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] how is pH treated in Amber - other than constant pH
> > simulations
> >
> > simulations in amber are either constant pH or constant protonation.
> > default protonations are reasonable for the isolated amino acids, but
> > pka shifts may occur in proteins. it is possible to calculate pkas for
> > the initial structure, assign protonation states, and keep them. this
> > is ok as long as there are not conformation dependent pka changes that
> > cross your pH.
> >
> > On 4/16/10, Andrew Voronkov wrote:
> >> Dear Amber users,
> >> when I am looking for questions about pH and Amber I get mostly information
> >> about constant pH simulations. But what pH is supposed to be by default,
> >> without constant pH simulations? Just neutral or what it depends from?
> >> As I understand in Amber pH is mostly set by protonation state of the
> >> molecules, so if not going to constant pH simulation I can approximately
> >> imitate some pH by setting corresponding protonation state distribution of
> >> amino acids. If physiological pH is required for protein simulation what can
> >> be general recommendation here - instant pH or default pH treatment?
> >>
> >> Sincerely yours,
> >> Andrew
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> > --
> > ===================================================================
> > Carlos L. Simmerling, Ph.D.
> > Professor, Department of Chemistry
> > CMM Bldg, Room G80 Phone: (631) 632-1336 Fax: 632-1555
> > Stony Brook University E-mail: carlos.simmerling.gmail.com
> > Stony Brook, NY 11794-5115 Web: http://www.simmerlinglab.org
> > ===================================================================
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
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Received on Tue Apr 20 2010 - 06:30:06 PDT
