AMBER: antechamber, how does it work

From: Francesco Pietra <>
Date: Wed, 15 Aug 2007 01:43:45 -0700 (PDT)

After consultation of Amber9 manual, Antechamber web page, and amber mailing
list, still it is not clear to me how antechamber works. I mean, to the end of
using it proficiently.

Amber9 manual (p 74, 4.1.1) lists divcon as a program called by antechamber. In
fact, during the AM1 minimization process, keywords of divcon (Amber9 manual p
213 on) are listed with values at each step.

My questions:

(1) Can divcon be launched selectively with amber (and an important option for
RESTARTING should a crash occur), or AM1 is what can be launched? It seems to
me that it is not the same thing.

(2) When launching antechamber as in tutorial B4 (the - more or less - way I am
using it), is "divide and conquer" at work? I see, during present antechamber
job, listed in divcon.out statements like "Resetting search direction". What
does that mean? That guess Hessian is recomputed from the last good
coordinates? Or does that mean that minimization of my molecule is done by
formally cutting it into pieces (divide and conquer)? The way I was used at
when computing charges "ab initio" via HF-6-31G* by formally cutting the
molecule into residues.

(3) Amber9 manual, after stating that divcon is called by antechamber (p 74),
refers to AM1 in the following pages, none of the many options of divcon
(chapter 7) being mentioned.

(4) When launching a QMMM procedure from sander.MPI, is the QM part running
parallel? If so, why not applying parallelization for the AM1 minimization
within antechamber?

This is a message from a user who has to rely heavily on antechamber, and is
carrying out a job for a non-polymeric, flexible molecule made of 500 atoms
with a huge number of chiral centers and many charges. Just the job of creating
a pdb file was real "work". I omit discussing why I am not using an external
program parallelized in AM1. Who had ever to prepare files for MD for large,
flexible non-polymeric molecule will understand why.


francesco pietra

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Received on Sun Aug 19 2007 - 06:07:04 PDT
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