AMBER Archive (2007)

Subject: Re: AMBER: divcon missing in Antechamber 1.27

From: David A. Case (case_at_scripps.edu)
Date: Mon May 28 2007 - 20:33:52 CDT

On Mon, May 28, 2007, Neelanjana Sengupta wrote:
>
> I downloaded Antechamber Version 1.27 from the Amber website. It looks like
> divcon is missing from this version... When I try Ross Walker's tutorial
> with sustiva, ie. I type the command,
>
> $AMBERHOME/exe/antechamber -i sustiva.pdb -fi pdb -o sustiva.prepin -fo
> prepi -c bcc -s 2
>
> I get this output:
> ====================
> Running: /w1/antech127/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o
> ANTECHAMBER_BOND_TYPE.AC -f ac -j full
>
> Running: /w1/antech127/exe/atomtype -i ANTECHAMBER_AC.AC0 -o
> ANTECHAMBER_AC.AC -p gaff
>
> Total number of electrons: 160; net charge: 0
>
> Running: $AMBERHOME/exe/divcon
> sh: /w1/antech127/exe/divcon: No such file or directory
> Error: cannot run "$AMBERHOME/exe/divcon" of bcc() in charge.c properly,
> exit
> ====================
> Please let me know what the issue is here...
>

You are mixing up the Amber version of antechamber and the "stand-alone" one.
The version shipped with Amber runs from $AMBERHOME/exe and invokes divcon
to do the semi-empirical calculations.

The standalone version (from http://amber.scripps.edu/antechamber) does
not require an Amber installation. It runs from $ACHOME/bin, and invokes
mopac6 for the semiempirical calculations. See the documentation that comes
with the antechamber tar file for installation instructions.

There are plusses and minuses to each of these semi-empirical programs, but
you have to choose one or the other. From your mail, it looks like you are
running the Amber version(?). You don't say which release of Amber you are
using, but an Amber 9 installation should have a divcon executable in
$AMBERHOME/exe.

Note also that the tutorial one the Amber web site refers to the Amber
version. You will have to make (trivial) changes to use it with the
stand-alone version (e.g. replace $AMBERHOME with $ACHOME).

...hope this helps....dac

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