By default, terminal residue is modeled in charged form. Neutral form could
be developed as described in
http://archive.ambermd.org/200606/0080.html
On Tue, Apr 20, 2010 at 3:27 PM, Andrew Voronkov <drugdesign.yandex.ru>wrote:
> 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
> > > > >>
> > > > >>
> > > > >>
> > > > >> _______________________________________________
> > > > >> AMBER mailing list
> > > > >> AMBER.ambermd.org
> > > > >> http://lists.ambermd.org/mailman/listinfo/amber
> > > > >>
> > > > >>
> > > > >
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > >
> > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Dmitry Nilov,
> > Lomonosov Moscow State University
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Dmitry Nilov,
Lomonosov Moscow State University
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Apr 20 2010 - 05:00:04 PDT
