AMBER Archive (2008)

Subject: AMBER: AMBER10 AMBERTools antechamber

From: Starr Hazard (hazards_at_musc.edu)
Date: Tue Dec 23 2008 - 10:36:05 CST

Folks,

I successfully compiled and tested AMBER10 and AmberTools 1.2 in directory

/One/Two/COMPILE/amber10

Then I moved the binaries to

/Three/Four/amber10/bin

So that other users and my compute nodes could see them. The new
$AMBERHOME is defined as /Three/Four/amber10/

I have been working with XLEAP and SANDER. The Benchmarks run and
Tutorial Basic 8 seemed fine

$AMBERHOME/bin/antechamber -help

Shows the ANTECHAMBER help menu

However, when I attempt to run the basic tutorial #4
http://ambermd.org/tutorials/basic/tutorial4/

The antechamber seems to be using the path to the compile directory to
locate "bondtype" and exits.

There does not appear to be an "option" way to tell ANTECHAMBER where
to look for executable and its default is to look where was compiled.

Will I have to recompile AmberTools in the final path in order for
ANTECHAMBER to find its binaries?

Starr

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