On Fri, Nov 21, 2014, Maria Diaz wrote:
>
> we want to carry out MD simulations for a cyclic peptide using
> amber. The cyclic peptide we are currently study has a bond between
> (modified) side chains of two amino acids (i.e. N-terminus or first
> amino acid and sixth residue). How can I parametrized the modified
> residues?
For the "antechamber" route to developing parameters for modified amino acids,
see both tutorial B4, and this page:
http://ambermd.org/antechamber/pro4.html
You might also want to use the R.E.D. server: see the link at the Amber web
page.
...good luck....dac
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Received on Fri Nov 21 2014 - 04:30:02 PST
