Re: AMBER: antechamber, how does it work

From: Francesco Pietra <>
Date: Wed, 15 Aug 2007 07:25:12 -0700 (PDT)

Hi Junmei. Thanks. Please, read below at your convenience.

--- Junmei Wang <> wrote:

> Antechamber mainly uses Divcon to generate AM1 or CM2 charges after
> structural optimization. Other functions of Divcon do not directly related to
> the antechamber package.

> If the molecule is big and sometimes restarting or multiple processes is
> needed, one may first generate divcon output (divout) and use it as input of
> antechamber.

I fear I do not understand here. Do you mean divcon.out file brought to
completion? After 48 hours, divcon.out is still in development, as follows:


ENERGY -3019.062736 GNORM = 406.233 GRDMAX = 63.8357 GRDAVR = 8.0472 DELTAE =
-64.038478 DELTAX = 0.011914


CYCLE = 2442
ENERGY = -3163.884775 GNORM = 0.931 GRDMAX = 0.2200 GRDAVR = 0.0150 DELTAE =
-0.000870 DELTAX = 0.000192

User supplied was:

Is it any hope to brought the calculation successfully to end? At any event,
could you please adjust your suggestion "one may first generate divcon output
(divout) and use it as input of antechamber" to the present situation?

Also, what about your "restarting or multiple processes" above? What I said, is
that sometimes "Resetting search direction" appears in the divcon.out file.

Please, remember that it is a non-polymeric molecule, so features for proteins
or DNA do not apply.


francesco pietra

> Mopac is another choice used by antechamber to generate AM1 and AM1-BCC
> charges.


> Best
> Junmei
> Francesco Pietra <> wrote:
> 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.
> Thanks
> francesco pietra
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Received on Sun Aug 19 2007 - 06:07:07 PDT
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