AMBER Archive (2009)

Subject: Re: [AMBER] install ambertools

From: case (case_at_biomaps.rutgers.edu)
Date: Thu Sep 17 2009 - 08:40:28 CDT

On Thu, Sep 17, 2009, Karl Kirschner wrote:
>
> We have been reorganizing our programs directory here at work. When we
> recompiled ambertool-1.2, with bug patches 1-8, we noticed that there were
> two directories for executables: $AMBERHOME/bin and $AMBERHOME/exe. The /bin
> directory had up-to-date time stamps on all of the files except teleap and
> xaleap. However, the /exe directory had old time stamps on all of the files
> except teleap and xaleap, which had the up-to-date time stamps.

$AMBERHOME/bin and $AMBERHOME/exe are supposed to be links to each other.
We are in the process of changing everything to "bin", but this is a stopgap.

The configure_at script does this:

if [ ! -x exe ]; then
    ln -s bin exe
fi

My guess is that somehow you put the new code on top of an old
installation, that already had an exe directory, so that the link was not
made. Get rid of the exe directory, and reconfigure and recompile.

...dac

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