On Mon, Aug 14, 2006, Amarda Shehu wrote:
>
>
> I want to construct a short peptide chain, adding peptide bonds as seeing
> fit. When I try to form a peptide bond between residue x and residue y with
> the command BOND mol.x.C mol.y.N, I get the following:
> Building proper torsion parameters.
> ** No torsion terms for CT-N3-C-CT
>
> I am not sure how to suppress amber from adding hydrogens first of all to
> my initial pdb file, and then how to tell it to add a peptide bond between
> two arbitrary residues.
>
By default, Amber makes the first and last residues of a peptide chain
"terminal" (e.g. with extra hydrogens on the N-terminus.). Change this by
editing your leaprc file and changing (or removing) the "addPdbResMap"
section.
It looks like your bond command worked; you just need to make sure that
residues that should be non-terminal are indeed non-terminal.
...dac
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Received on Wed Aug 16 2006 - 06:07:12 PDT
