On Fri, Jan 27, 2012, James Starlight wrote:
> 1- I need to find special triplet motif ( e.g Thr-Leu-Gly) in my big protein.
>
> 2- In this motiv I want to create new Covalent bond between 2 adjacent
> atoms ( e.g N atom in Gly and C atom in Thr) ( distance 1 A) and than
> make geometry optimisation of this new motif.
You will end up with an unusual cyclic peptide portion with a
five-membered ring, as far as I can see. The chemistry you are proposing
is not very clear to me, (not that it needs to be), but if you want this
to be a part of a "big protein", you probably need to define (and get
force field parameters for) a special "residue" that is the cyclic TLG
combination. I'd start small, and construct a model for just the cyclic
tripeptide all by itself, and make that do what looks correct; then as a
second step, incorporate that motif into a bigger peptide.
Antechamber or the R.E.D. server can help you out with the first task.
....good luck....dac
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Received on Fri Jan 27 2012 - 12:30:02 PST
