Re: [AMBER] problem to apply AmberTools patch 7 and induced crash of the whole Amber14 installation process

From: Jason Swails <>
Date: Mon, 28 Jul 2014 09:58:21 -0400

On Mon, Jul 28, 2014 at 7:49 AM, Marc van der Kamp <
> wrote:

> Hi,
> I've experienced the same problem with applying update.7.
> It looks like it is a problem with the patch; I've tried this on our local
> cluster (Rocks 5.3 - Essentially RedHat) and on my MacBook (MacOS 10.7.5).
> In both cases, the patch failed to apply:
> $ ./update_amber --update
> Preparing to apply updates... please wait.
> Downloading updates for AmberTools 14
> Downloading AmberTools 14/update.7 (192.92 KB)
> Downloading: [::::::::::::::::::::::::::::::::::::::::::::::::::] 100.0%
> Done.
> Applying AmberTools 14/update.7
> instance: .patches/AmberTools14_Unapplied_Patches/update.7 failed to apply.
> No changes made from this patch

​OK, I was actually unaware of this (but I've been traveling the past few
days). I found the problem and fixed it. The updating script did not make
any changes from this patch, but it did cache the patch file to avoid
having to go online and re-download it. Since you _want_ update_amber to
go online and re-download it, you have to tell update_amber to delete any
unapplied patches for specifically that reason. So make sure you run the

./update_amber --remove-unapplied

before trying to reconfigure and recompile.

Let me know if you run into any problems.

All the best,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Mon Jul 28 2014 - 07:30:02 PDT
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