I had same error. Sounds like ./update_amber --upgrade
is not robust to all prior patching pathways. I can't say what I did
that was not according to the canonical patch procedure. I tried to
follow what Dr. Case outlined, and there were no errors during the
./patch_amber.py --update
step. But in any case, I guess I screwed up somehow. Not a big problem
to just download 13 anew.
Bud Dodson
On Apr 22, 2013, at 7:09 PM, Jonathan Gough wrote:
> same issue on my laptop here at home. weird.
>
> So your saying to just start from scratch again with Amber12 and
> AmberTools13?
>
>
> On Mon, Apr 22, 2013 at 6:59 PM, Jason Swails <jason.swails.gmail.com>wrote:
>
>> On Mon, Apr 22, 2013 at 6:45 PM, Jonathan Gough
>> <jonathan.d.gough.gmail.com>wrote:
>>
>>> no changes. I actually untarred amber12 and ambertools12 and started
>> from
>>> scratch. then i tried to do the update to ambertools13.
>>>
>>> I had some sort of error regarding bugfix16 that I couldn't figure out
>> so I
>>> started from scratch.
>>>
>>
>> Hmm... I can't reproduce this behavior. A simple solution is to just
>> download the AmberTools13.tar.bz2 file and untar that alongside
>> Amber12.tar.bz2.
>>
>> This is the way upgrades were traditionally handled. While this is the
>> slower route, it will give you exactly the same code.
>>
>> Good luck,
>> Jason
>>
>> --
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Candidate
>> 352-392-4032
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
M. L. Dodson
Business email: activesitedynamics-at-gmail-dot-com
Personal email: mldodson-at-comcast-dot-net
Gmail: mlesterdodson-at-gmail-dot-com
Phone: eight_three_two-five_63-386_one
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Apr 22 2013 - 17:30:03 PDT
