Re: [AMBER] cyclic peptide

From: FyD <>
Date: Thu, 09 Dec 2010 15:42:34 +0100

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:
You go . "Charge value comparison" in the graphical interface:
   and click on

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

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 - 07:00:02 PST
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