AMBER Archive (2009)

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

From: Brothers, Michael Charles (
Date: Wed Jun 10 2009 - 14:40:21 CDT

I used the following command in all lower case letters:

Antechamber -I test2.pdb -fi pdb -o test2.mol2 -fo mol2 -c bcc

I know that antechamber was designed mainly for small organic molecules, but what I have here is a small organic molecule covalently bound to a peptide. My input file is "only" 4-15 residues long. If I could generate the force field for the ligand separately and then incorporate it, that would also work (I'm assuming I would use LEaP for the generation of the force field for the helices I'm using). I'd prefer avoiding manual input, but if its necessary, then it'll have to be done,



-----Original Message-----
From: [] On Behalf Of David A. Case
Sent: Wednesday, June 10, 2009 12:24 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Generating LeAP file for helix containing non-standard amino acid

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


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