Re: [AMBER] update error

From: Jason Swails <>
Date: Mon, 11 Nov 2013 07:16:38 -0500

On Mon, 2013-11-11 at 11:55 +0530, Raman Parkesh wrote:
> Dear All,
> I am compiling Amber12 and Ambertools 13 in the CentOS 6.4 system with
> graphics card GTX770, which is supported for GPU MD calculations.
> I compilied the cuda and was able to run ./deviceQuery, which works fine.
> CUDA_HOME path is set.
> However, I had problems in compiling amber cuda and after a while I
> realized that amber 12 was not updated (only 1-8 bugfixes were updated)
> Here is the problem I get when I do amber update. It gives error at bugfix
> 9 which is below:
> *Applying Amber 12/bugfix.9.bz2BadPatchError: Could not decompressing
> .patches/Amber_Unapplied_Patches/bugfix.9.bz2 with bunzip2.*
> I think there is some file name error??

Not likely. My guess is that you do not have the program "bunzip2"
which is necessary to decompress .bz2-compressed patch files.

Make sure you have access to this program. What does the command

which bunzip2


> I got a suggestion from Jason Wiki and I downloaded bugfix 9 to 21 in the
> folder and placed in the directory /home/samvit/amber12/updates in my local
> machine and then as suggested did this
> ./update_amber --amber-updates=/home/samvit/amber12/updates
> But then nothing happens. I think I am missing something here.

All this does is tell update_amber that it should look for Amber updates
in that folder. You still need to run

./update_amber --update

if you want those updates to be applied.

Good luck,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Mon Nov 11 2013 - 04:30:03 PST
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