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 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?
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:
GAM-PRO-X-X-...PHE
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 Thu Dec 09 2010 - 10:00:04 PST
