AMBER Archive (2009)

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

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Wed Jun 10 2009 - 14:23:36 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
> "path -j full - I ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC
> -f ac" in judgebondtype() of antechamber.c properly, exit.

!!Aargh -- typos corrected below!!

You don't really say what commands you gave to antechamber, but please remember
that antechamber is designed to look a *single* residues, not at entire
peptides. See the examples in http://ambermd.org/antechamber/example.html.

....dac

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