Re: AMBER: antechamber

From: Francesco Pietra <>
Date: Mon, 9 Jul 2007 14:57:45 -0700 (PDT)

I have treated with Amber9/Antechamber a molecule (natural product, 98 atoms)
made of two residues (because I had used another suite of programs to calculate
RESP charges, which required to make smaller residues, and pdb atom names were

I expected failure of antechamber. Actually, it prepared valid parameter and
coordinate files, that allowed correct minimizations."list" on the prepin file
showed as new unit the first of the two residues, in three capital letters. At
all stages, generation of pdb files gave the correct molecule on VMD.

Perhaps what I did is not the equivalent of what is here warned about, althoug
my molecule is seen as two residues on the original suite where the arragement
was done.

francesco pietra

--- "David A. Case" <> wrote:

> On Mon, Jul 09, 2007, Marie Brut wrote:
> > I prepared a mol2 file containing the coordinates of a small double strand
> > of DNA. Then, I used antechamber to generate a prepin file but here is the
> > problem : until the end of the first strand, everything is normal, but
> after
> > the prepin file is like this :
> Antechamber is designed to work on single residues only. It won't work for
> multiple strand molecules. You will need to split the input for antehchamber
> up into pieces, then recombine them later in leap.
> ....dac
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Received on Wed Jul 11 2007 - 06:07:35 PDT
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