Hi,
As long as your AMBERHOME environment variable points to the new AT12
directory and your PATH contains the bin directory of AT12 you should
be fine.
-Dan
On Wed, Jan 23, 2013 at 3:53 PM, Kamali Sripathi <ksripath.umich.edu> wrote:
> Thanks Jason and Dan. Quick question: aside from pathname confusion, is
> there any reason why I shouldn't have AT1.4 and AT12 on my computer at the
> same time? I'm not really sure of the most effective way to uninstall
> AT1.4, and I wouldn't want to waste time figuring it out.
>
> Dan, you were right: my raw production files are ~ 2.6 GB, so the bugfix
> might just fix everything.
>
> Thanks so much again,
>
> Kamali
>
> On Wed, Jan 23, 2013 at 10:31 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> Hi,
>>
>> There was an issue in AT1.4 ptraj when determining the number of
>> frames in large (> 2GB) GZ-compressed Amber trajectories that was
>> addressed by bugfix 16. Make sure you've applied all the AT 1.4
>> bugfixes (http://ambermd.org/bugfixesat.html).
>>
>> However, as Jason said, upgrading to AmberTools12 is probably your
>> best bet (http://ambermd.org/AmberTools-get.html).
>>
>> -Dan
>>
>> On Wed, Jan 23, 2013 at 5:52 AM, Kamali Sripathi <ksripath.umich.edu>
>> wrote:
>> > Dear AMBER users,
>> >
>> > I've found a problem when analyzing AMBER10 trajectories using
>> > AmberTools1.4 on my personal computer. I get this error:
>> >
>> > *PTRAJ: trajin production1.traj.gz*
>> > * Checking coordinates: production1.traj.gz*
>> > *checkCoordinates(): Could not predict number of frames for AMBER
>> > trajectory file: production1.traj.gz*
>> > * If this is not a compressed file then there is a problem*
>> > *Rank: 0 Atoms: 58226 FrameSize: 1414917 TitleSize: 81 NumBox: 3
>> Seekable 0*
>> >
>> > which I know typically indicates that the topology and trajectory files
>> fed
>> > into ptraj are different. I know that can't be the problem in my case,
>> > however, since I use the same topology file that I used to write the
>> > trajectory in the first place, and I've successfully used this pair with
>> > ptraj on a different cluster. I have to assume, then, that the problem is
>> > because my production files are written using AMBER10, and the AmberTools
>> > on my computer is version 1.4. Interestingly, I do not see this error
>> when
>> > analyzing joined, stripped trajectories from the same simulation.
>> >
>> > I was wondering if there was patch or modification I could apply that
>> would
>> > let me analyze raw trajectories on my computer using the newer version of
>> > AmberTools? I've looked a bit in the mailing list archives and in the
>> > AmberTools manual, but haven't found an answer to my question so far.
>> > Please do let me know if I've missed something, however.
>> >
>> > Thank you all, and have a great day,
>> > --
>> > Kamali Sripathi
>> > PhD Candidate, Medicinal Chemistry
>> > Walter Laboratory
>> > 930 North University
>> > Ann Arbor, MI, 48109
>> > ksripath.umich.edu
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 201
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-9119 (Fax)
>>
>> _______________________________________________
>> 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
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Wed Jan 23 2013 - 15:30:03 PST
