Thanks again, Dan and Jason for your replies, and sorry for my late one.
This discussion has been incredibly helpful!
Thank you all so much and have a great weekend,
Kamali
On Wed, Jan 23, 2013 at 6:18 PM, Jason Swails <jason.swails.gmail.com>wrote:
> 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
>
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Received on Sat Jan 26 2013 - 07:00:03 PST
