Jason,
Thanks for this. As you said I realized the possibility of broken amber
tree so deleted the old amber12 directory and started a fresh copy of
amber12 and was able to update with the command
./update_amber --update
Configuration with gnu and make install went fine. Make test is going on
and seems fine.
I hope cuda compilation will go smoothly this time. Will keep udated about
the progress.
Cheers,
Raman
On 11 November 2013 17:42, Jason Swails <jason.swails.gmail.com> wrote:
> 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.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Mon Nov 11 2013 - 05:30:02 PST
