On Mon, Aug 1, 2011 at 4:03 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Mon, Aug 01, 2011, Massimiliano Porrini wrote:
> >
> > Since it was not me to install both Amber and AmberTools in the
> > cluster I am running on, is there any way to check which version I am
> using?
> >
> > And in case I am using the not fixed version 1.4, how can I
> > patch it?
>
> Either (a) go to http://ambermd.org, click on "bug fixes" and follow the
> instructions to patch version 1.4; or (b) download AmberTools1.5 from the
> same
> web site. I would recommend the latter.
>
> [I don't think there is any easy way to determine which version someone
> else
> installed, although Jason probably knows....]
It's not nearly as good as a --version flag, but the following can help tell
what version you have (as long as you haven't done anything like renaming
directories and adding/removing files and directories):
If you have AmberTools 1.2, then it unpacks into an amber10/ directory and
builds alongside amber10.
If you have AmberTools 1.3, then it unpacks into an amber11/ directory, but
I don't think it can build with Amber11. In any case, it's unlikely anybody
is using this version. (since it was only ~6 months between 1.3 and 1.4
releases IIRC)
If you have AmberTools 1.4, then it unpacks into an amber11/ directory, and
it *can* build with Amber11. Furthermore, it has no
$AMBERHOME/AmberTools/src/cpptraj/ directory or $AMBERHOME/AT15_Amber11.py
script.
If you have AmberTools 1.5, then it unpacks into an amber11/ directory and
it *can* build with Amber11 as long as you run AT15_Amber11.py, and it
*does* have a cpptraj directory. This is also the first release to build
mdgx by default, IIRC.
If you're just trying to distinguish between AT 1.4 and AT 1.5, look for the
cpptraj and mmpbsa_py directories in $AMBERHOME/AmberTools/src and the
AT15_Amber11.py script (these are only in AmberTools 1.5). (The easiest
file to trace, though, is probably the configure file, if you know what to
look for).
The only packages you can download right *now* are AmberTools 1.5 and
AmberTools 1.2 (to build amber10).
Looking at git logs, it appears as though Mengjuei fixed tleap's huge
segfaulting issue (caused by 64-bit builds) ~6/1/2010. So it appears that
anything older than AmberTools 1.4 will experience frequent segfaults with
tleap.
Perhaps we should add the AmberTools version to *something*? Each package's
Makefiles? Require each package to recognize a --version flag? The master
Makefile?
Of course if you have the original tarball it says there.
I don't know how helpful this is. (To Massimiliano, I suggest that you
build your own AmberTools 1.5, since that's the package that will get the
most support. If something doesn't work in older versions, the maintainer
will probably just ask you to upgrade to see if the problem goes away,
anyway).
HTH,
Jason
> ....dac
>
>
> _______________________________________________
> 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 Mon Aug 01 2011 - 14:00:03 PDT
