AMBER Archive (2006)

Subject: Re: AMBER: problem imposing arbitrary peptide bonds through leap

From: David A. Case (
Date: Mon Aug 14 2006 - 11:45:48 CDT

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"

It looks like your bond command worked; you just need to make sure that
residues that should be non-terminal are indeed non-terminal.

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