Sorry if I was unclear. What I meant is something like this:
X - (N)PRO-CO-CH2-CH2-CH2-NH-(C)PHE-X
| |
X - X - X - X - X - X
with NPRO and CPHE i meant that CO and NH in the semplification above are
not respectively those of PRO and PHE.
.Dr Case: what I did using ACE and NME and then changing an hydrogen of ACE
mehyl group to a carbon isn't similar of drawning CO-CH2-CH2-CH2-NH ? I
thought I only had to use then the command "bond". What about it?
2010/12/9 FyD <fyd.q4md-forcefieldtools.org>
> Dear Dr Case, dear Rossella,
>
> I might have overlooked what Rossella asked, sorry. But the strategy
> remains identical to what I proposed in my former email.
>
> One builds a molecular fragment from a whole molecule:
>
> R1-CH2-CH2-CH2-R2 --> CH2-CH2-CH2
> <--> <-->
> (1) (2)
> (1) & (2): two intra-molecular charge constraints = 0
>
> The key is to correctly select the R1 & R2 chemical groups. I would
> start using once again ACE (MeCO for a ketone) and NME (NHMe for an
> amine). The statistic module of R.E.D. Server should provide the
> answer if "yes" or "no" these ACE & NME capping groups are suitable to
> generate the CH2-CH2-CH2 building block in your case.
>
> See for instance:
> http://q4md-forcefieldtools.org/REDS/faq.php
> http://q4md-forcefieldtools.org/REDS/faq.php#1
> then
> http://q4md-forcefieldtools.org/Tutorial/DNA-FFTopDB/P1.html
> You go . "Charge value comparison" in the graphical interface:
> and click on
>
> http://q4md-forcefieldtools.org/Tutorial/DNA-FFTopDB/P1/Data-R.E.D.Server/Mol_MM/stat-RESP-FIT_mm
>
> In this example, you get charge values obtained for a whole molecule
> without constraint versus a multiple molecule charge fit with charge
> constraint... The same type of file is generated when a single
> molecule is involved in the fit with intra-molecular charge constraint
> versus without intra-molecular charge constraint.
>
> [Finally we could also imagine to rebuild the central fragments of PRO
> and PHE (same approach as above; may-be even the best bet) since they
> were originally built to connect an amide; and not a ketone and an
> amine]
>
> regards, Francois
>
>
> >> I have to build a cyclic peptide, the two terminals aminoacids are N-PRO
> and
> >> C-PHE and they are linked togheter by CO-(CH2)3-NH. So the sequence
> should
> >> be:
> >> ...-PRO-CO-CH2-CH2-CH2-NH-PHE-...
> >> How can I build it?
> >> I tried making a linear sequence with ACE-PRO-.....-PHE-NME and then I
> >> turned (but just with the command draw in the unit editor) an hydrogen
> of
> >> ACE in a carbon with the idea of using then the command bond, but
> probably I
> >> have instead to create a new unit modified of ACE with the right
> parameters
> >> for the new methil group... is it right? and if it's so, how can I
> create
> >> this new unit?
> >
> > First, don't add ACE and NME, since it sounds like you don't want those.
> > But I'm confused about the exact structure you wish to build. What you
> show
> > above seems to have PRO as the final residue of the peptide (it seems to
> be
> > conncted to some previous amino acid, and ends with a CO); but you
> > text refers
> > to N-PRO. If you can't figure it out, you will have to post the full
> > structure you are trying to create. (Apologies if I am missing something
> > obvious here.)
> >
> > Second, copy your leaprc file to a new location, and edit the copy to
> remove
> > the addPdbResMap section. This will prevent the end residues from having
> NH3
> > or CO2 additions.
> >
> > Third, in xleap draw in the CH2-CH2-CH2 groups between the PRO and PHE.
> This
> > may be tricky if you don't have any initial structure, but you can
> > create some
> > long bonds, and hope they get fixed up in minimization/dynamics. Make
> the
> > carbon atoms type CT and the hydrogens type HC. You could start with
> zero
> > charges on these atoms, or use RED or a similar tool to try to get resp
> > charges.
> >
> > This is just an outline...don't be afraid to experiment!
> >
> > ...good luck...dac
>
>
>
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Received on Thu Dec 09 2010 - 08:00:03 PST
