Re: [AMBER] ambertools14 fresh installation fails

From: Jason Swails <>
Date: Tue, 27 Jan 2015 11:33:54 -0500

On Tue, Jan 27, 2015 at 10:47 AM, David A Case <>

> On Tue, Jan 27, 2015, Fabian Glaser wrote:
> > Available AmberTools 14 patches:
> >
> > update.6, update.7, update.8, update.9, update.10, update.11, update.12,
> > update.13, update.14.bz2, update.15,
> looks suspicious, since updates 1 to 5 are not listed. Are you sure you
> do not have a directory $AMBERHOME/.patches? Note that since the directory
> name begins with ".", you must use the -a flag to "ls" in order to see it.

‚ÄčThis diagnosis looks correct to me. update_amber uses a ".patches/"
directory inside $AMBERHOME to keep track of updates that have been
downloaded and applied (this also makes it possible to *reverse* updates
when desired, since they are stored locally). And update_amber assumes a
certain naming and numbering scheme for updates, so it will not try to look
for update.6 unless it already thinks updates 1 through 5 have been
applied. Which means that you almost certainly have an
$AMBERHOME/.patches/AmberTools14_Applied_Patches directory with (at least)
the file update.5 present.

‚ÄčThe only way I can think of this happening is that you had a copy of
AmberTools 14 installed with the first 5 updates applied. Then you wanted
to start over, so you extracted AmberTools14.tar.bz2 into the same amber14
directory, overwriting all of the files inside AmberTools14.tar.bz2 with
their original versions, but not actually deleting any of the
already-existing files that were created during past installations.

As a result, update_amber *thinks* the first 5 updates have been installed,
but they really haven't (and update.6 makes changes on top of the changes
from update.2, so if update.2 has *not* been applied, trying to apply
update.6 will fail).

If this is, indeed, what you did, the only way out now is to completely
delete the amber14 directory (rm -fr amber14) and untar the
AmberTools14.tar.bz2 tarball into a fresh directory. As a note for the
future: update_amber is fairly robust in what it does, such that it always
keeps track of all updates it creates, and you can use
"$AMBERHOME/update_amber --version" to see how many updates have been
applied to both Amber and AmberTools (or "$AMBERHOME/update_amber
--show-applied-patches" for a more detailed view).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Tue Jan 27 2015 - 09:00:02 PST
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