AMBER Archive (2009)

Subject: Re: [AMBER] Generating LeAP file for helix containing non-standard amino acid

From: David A. Case (
Date: Wed Jun 10 2009 - 14:14:49 CDT

On Wed, Jun 10, 2009, Brothers, Michael Charles wrote:
> I am having issues generating an amber force field for a protein
> containing my non-standard amino acid. I generated the helix itself in
> Macromodel and then modified the amino acid to my side chain (Cysteine
> -> Cys + side-chain, labeled DMV in this model).
> I tried changing HETATOM to ATOM and moving the terminal residue to the
> end, but it didn't seem to significantly help (although it did try to
> compile the force field before giving an output of "Error: cannot run
> -f ac" in judgebondtype() of antechamber.c properly, exit.

You don't really way what commands to gave to antechamber, but please remember
that antechamber is designed to look a *single* residues, not at entire
peptides. See the examples in


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