Yes, I have found none in manual and I wonder what is generally done in this case and if this was somehow considered.
20.04.10, 14:43, "Dmitry Nilov" <nilovdm.gmail.com>:
> Hello! There are no standard uncharged N-terminal and C-terminal residues in
> Amber.
>
> On Tue, Apr 20, 2010 at 2:23 PM, Andrew Voronkov wrote:
>
> > A bit more general question. For example I've got pKa which correspond to
> > protonated state of amido group of N-terminal amino acid or deprotonated
> > state of C-term carboxylic group. How is possible in amber to discriminate
> > by names between protonated\deprotonated C- and N- terminal amido and
> > carboxylic groups?
> >
> > Best regards,
> > Andrew
> >
> > 16.04.10, 15:05, "Dean Cuebas" :
> >
> > >
> > > > From: Andrew Voronkov
> > > > Reply-To: AMBER Mailing List
> > > > Date: Fri, 16 Apr 2010 13:17:32 -0500
> > > > To: AMBER Mailing List
> > > > Subject: Re: Re: [AMBER] how is pH treated in Amber - other than
> > constant pH
> > > > simulations
> > > >
> > > > Thank you that is actually what I do. The prediction by H++ server
> > with
> > > > isntant protonation, just wondered if this fits to Amber pH strategy
> > without
> > > > constant pH. As to H-bonds from Molprbity - aren't H bonds supposed to
> > result
> > > > mostly from MD simulations?
> > >
> > > I might have been a bit confusing here...
> > > What I meant was that the way that molprobity (the reduce app) adds
> > > hydrogens to especially histidine tends to be better than H++ in that it
> > > assigns delta versus epsilon tautomers. In fact, I've only seen H++
> > > assigning uncharged histidines as epsilon, whereas reduce will assign
> > delta
> > > and visually it is very clear that a strong H-bond from another residue
> > to
> > > the delta H of a particular HIS is clearly preferred over an epsilon
> > without
> > > such h-bond stabilization. On the other hand, H++ pka predictions
> > usually
> > > help with deciding to have protons on both delta and epsilon nitrogens.
> > >
> > > Of course you can go the whole mile and do an iterative process where
> > you
> > > now do MD on your first set of protonation predictions and then resubmit
> > to
> > > molprobity and H++ to see if you converge on a stable set of
> > predictions.
> > >
> > > Dean
> > > > Btw as I can see many parameters like Z-score significantly improve
> > after MD
> > > > even against X ray structures.
> > > >
> > > > Best regards,
> > > > Andrew
> > > >
> > > > 16.04.10, 11:53, "Dean Cuebas" :
> > > >
> > > >>
> > > >> 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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> > > >>
> > > >>
> > > >
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> > >
> > >
> > >
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> > >
> > >
> >
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> >
>
>
>
> --
> Dmitry Nilov,
> Lomonosov Moscow State University
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Received on Tue Apr 20 2010 - 04:30:02 PDT
