A little blurb about installing them side-by-side:
http://jswails.wikidot.com/installing-ambertools-12-and-older-amber
While it talks about an older Amber, it also applies to an older AmberTools.
Also, in order to 'uninstall' any version of Amber, just remove the whole
amberXX directory it's housed in (e.g., rm -fr amber11). Note this will
also get rid of any Amber installation in that directory, too. And you
can't delete just AmberTools, since some programs in Amber depend on
AmberTools being there (and the right version).
HTH,
Jason
On Wed, Jan 23, 2013 at 6:03 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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
Received on Wed Jan 23 2013 - 15:30:03 PST
