AMBER Archive (2009)

Subject: Re: [AMBER] divcon question

From: case (case_at_biomaps.rutgers.edu)
Date: Mon Aug 31 2009 - 07:34:14 CDT

On Mon, Aug 31, 2009, Andrei Neamtu wrote:
>
> I am trying to use Dock 6.3 with Amber scoring function. In the Dock
> manual it says it needs am working Amber installation.
> The test suite of dock stops with an error message that indicate that
> the divcon executable is missing in the $AMBERHOME/bin directory.
> The compilation of Amber 10 worked fine and passes all the tests
> including divcon tests (make test.sander.DIVCON).
>
> However I couldn't find a divcon executable in the amber directories..

The Amber distribution no longer creates a divcon executable; we use mopac
instead (to get AM1 Mulliken charges). The test.sander.DIVCON tests run
the version of divcon built-in to sander, not a stand-alone executable.

You should post the Dock-related questions to their mailing list. However, my
guess is that you have not set your DOCK_HOME environment variable. When this
is not set, the antechamber code in dock looks for an (old) set of executables
in AMBERHOME/bin.

Note to Scott: the requirement to set the DOCK_HOME variable is pretty easy to
miss. It is stated in dock6/install/test/README, but not in the Dock 6.3
Users Manual nor in the output of "configure -help". Beyond that, the
behavior in antechamber when AMBERHOME is set should probably be removed:
Dock has no way of knowing which version of Amber might be installed, and
should not try to use Amber executables, in my view.)

...good luck...dac

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