Re: [AMBER] cyclic peptide

From: case <>
Date: Thu, 9 Dec 2010 08:03:07 -0500

On Thu, Dec 09, 2010, Rossella Noschese wrote:

> 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

This is just an outline...don't be afraid to experiment!

...good luck...dac

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Received on Thu Dec 09 2010 - 05:30:02 PST
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