Re: [AMBER] update error

From: Jason Swails <>
Date: Mon, 11 Nov 2013 07:12:10 -0500

On Mon, 2013-11-11 at 15:14 +0530, Raman Parkesh wrote:
> Hi,
> Further to the update error, I manually downloaded the bugfixes and place
> them in the folder /home/samvit/bugfixes/12.0 and then manually updated
> them with the command
> ./update_amber --apply /home/samvit/bugfixes/12.0/bugfix xx
> It fixed upto bugfix 17 but I am not able to fix the bugfix 18.
> Preparing to apply a third-party update/patch... please wait.
> Applying bugfix.18.bz2
> PatchingError: .patches/ThirdParty12_Unapplied_Patches/bugfix.18 failed to
> apply. No changes made from this patch

Do not do this. The "--apply" flag is intended for third-party (and
other) extraneous patches, not for official updates. It is possible
that you have broken your tree and starting over from a fresh copy of
Amber 12 and AmberTools 13 is your best bet here.

If the [[--update]] flag does not work, either your code has been
changed in a way that is incompatible with the updates, there is a
missing program (like `patch', `bunzip2', or `gunzip') that update_amber
needs to apply various updates. These should be fixed.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Mon Nov 11 2013 - 04:30:02 PST
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