Re: [AMBER] cyclic peptide

From: Rossella Noschese <>
Date: Tue, 14 Dec 2010 14:29:46 +0100

dear dr. Case,

I made my model as I told you (modifying an hydrogen of ACE as to be a
carbon), and it's ok, I set the atom type as CT and charge as 0.0000. I used
the bond command, I manually erased the hydrogens on the carbons of this
bond (I thought they would be erased by default with the command bond, but
it wasn't so). However, I obtained my cyclic peptide. Pdb looks good. When I
calculate the net charge, it gives me a charge of -0.21 (the sum of the
charges of the hydrogen i erased on NME after binding and the hydrogen I
transformed in C on ACE whose charge I turned in 0.0000).
What about it?

2010/12/9 case <>

> On Thu, Dec 09, 2010, Rossella Noschese wrote:
> > 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
> > 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?
> Sounds OK to me. I think I misunderstood what direction the peptide chain
> was going earlier. Another way of
> thinking about this is that you have a modified amino acid residue:
> NH-CH2-CH2-CH2-CO. If this is correct(?) you have only amide connections,
> no ketones or amines (as Francois seems to think). There are tutorials
> (both
> for R.E.D. and for antechamber) that walk through the construction of a
> force
> field for modified amino acid residues. If you called this modified
> residue
> "GAM" (for gamma-amino-acid), then your peptide sequence would be:
> and you would then add a bond between the C atom of PHE and the N atom of
> GAM,
> giving the structure you want.
> ....good luck....dac
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Received on Tue Dec 14 2010 - 06:00:02 PST
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