Re: AMBER: antechamber

From: M. L. Dodson <>
Date: Mon, 09 Jul 2007 19:08:27 -0500

Francesco Pietra wrote:

> 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
> correct).
> 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

Hey, if it works, ... However, I think the point is that the
tools in the AMBER suite have specific things that they do. These
things are implicitly (actually quite explicitly) related to the
"model" of the kinds of molecules AMBER has been most often used
to simulate: biopolymers. That does not mean you cannot use AMBER
to simulate other molecule types, though. In the AMBER way of
looking at the world, molecules are small (e.g., ligands of
binding proteins) or polymers. Polymers are composed of
"residues" (e.g., nucleotide or amino acid residues). To compose
the input for the simulation programs (primarily sander and
pmemd), you use LEaP (i.e., tleap or xleap; the acronym relates
back to three older and obsolete AMBER programs). And of course
the residues are composed of atoms. So the hierarchy of things
AMBER knows about are atoms, residues and polymers. Ligands and
other small molecules can be thought of as residues that are
closed shell in the quantum chemistry sense.

So how do we get new residues? We use antechamber (or, these
days, maybe RED II or RED III). To create a residue descriptor,
you need the partial atomic charges which you get with a quantum
chemistry package, GAMESS or Gaussian mostly. But you need to do
a closed shell calculation with the QM package, so you may need to
add "capping residues". E.g., say we had a new amino acid
residue, XYZ. We might do a QM calculation on the closed shell
polymeric structure, {ACE XYZ NME}. Then to calculate the partial
charges of XYZ, we would constrain the atomic charges of ACE and
NME to 0.0 when running resp and define "connect" atoms where
other residues are connected to form the polymer structure.
Antechamber automates the steps in this new residue definition
procedure. A closed shell ligand or other small molecule is just
a residue with no connect atoms in this way of looking at things.

So the "AMBER way" to handle new molecules is to use antechamber
(or RED) to generate residue descriptors, then use LEaP to put the
residues together to generate the final molecules to be simulated,
together with counterions and solvent molecules if desired.

You can probably do it other ways, but this is the way I think of
when describing the "Amber way" of doing things. All of this is
in the documentation, but maybe not in two adjacent paragraphs.

Bud Dodson

> --- "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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M. L. Dodson
Email:	mldodson-at-houston-dot-rr-dot-com
Phone:	eight_three_two-five_63-386_one
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Received on Wed Jul 11 2007 - 06:07:37 PDT
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