AMBER Archive (2009)
Subject: RE: [AMBER] Generating LeAP file for helix containing non-standard amino acid
From: Brothers, Michael Charles (mcbroth_at_sandia.gov)
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,
On Wed, Jun 10, 2009, Brothers, Michael Charles wrote:
!!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.