RE: [AMBER] antechamber error

From: Mike Hanby <>
Date: Thu, 10 Dec 2009 16:34:30 -0600

Has anyone come up with a workaround for this while we wait for Amber 11? I distribute all software to our workstations via RPMs and have come up with a spec file that I _thought_ resulted in a working Amber and AmberTools distribution.

Apparently, none of the users over the past year have used antechamber (and I'm assuming there are other tools that suffer from the 'hard coding' of AMBERHOME). Sander, pmemd and other executables all work.

At any rate, here's the error reported by one of my users:

$ antechamber -i sustiva.pdb -fi pdb -o sustiva.mol2 -fo mol2 -c bcc -s 2
Cannot open connect_file /home/builder/rpm/BUILD/amber10/dat/antechamber/CONNECT.TPL in connect(), exit

Obviously, that's the path used during the build, but the software actually gets installed to /opt/amber10.

I'm wondering if anyone has a patch or suggestion to resolve this in the interim? I tried changing DATDIR in configure_at and configure_amber, however that caused build failures because the build attempts to copy files to the location, and only root has permissions to do that.

-----Original Message-----
From: [] On Behalf Of case
Sent: Wednesday, September 16, 2009 1:44 PM
To: AMBER Mailing List
Subject: Re: [AMBER] antechamber error

On Wed, Sep 16, 2009, Taufik Al-Sarraj wrote:

> i recently updated AMBER and i changed the directory's name from
> AMBER10.09 to AMBER10.25

If you changed the directory name after you compiled the program, you will
need to recompile -- it only takes a minute or so. The locations of
data files are entered into the program at compile time.

[For better or worse, this will change with the next release.]


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Received on Thu Dec 10 2009 - 15:00:13 PST
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