AMBER Archive (2009)

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

From: Brothers, Michael Charles (mcbroth_at_sandia.gov)
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,

Thanks,

Mike

-----Original Message-----
From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] 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 http://ambermd.org/antechamber/example.html.

....dac

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