Dear Jason and David,
Many thanks for the useful hints.
Following your advises, I decided to install AmberTools 1.5 in my local machine
and everything seemed to work fine.
All the tests passed, apart from those that required the installation
of Amber11 (sander),
as you can see:
481 file comparisons passed
2 file comparisons failed
0 tests experienced errors
Test log file saved as logs/test_at_serial/2011-08-02_20-21-38.log
Test diffs file saved as logs/test_at_serial/2011-08-02_20-21-38.diff
But unfortunately I got again segmentation fault with loadPdb in
executing the same
procedure I posted yesterday, that is:
:~>tleap
>source leaprc.ff99SBildn
>set default PBradii mbondi2
>loadOff seh.lib
>peptide = loadPdb peptide.pdb
This time I enclosed also the pdb file of the peptide (and my library
seh.library as well).
Any kind suggestion?
Cheers,
2011/8/1 Jason Swails <jason.swails.gmail.com>:
> 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
>
--
Dr Massimiliano Porrini
Institute for Condensed Matter and Complex Systems
School of Physics & Astronomy
The University of Edinburgh
James Clerk Maxwell Building
The King's Buildings
Mayfield Road
Edinburgh EH9 3JZ
Tel +44-(0)131-650-5229
E-mails : M.Porrini.ed.ac.uk
mozz76.gmail.com
maxp.iesl.forth.gr
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Aug 02 2011 - 14:00:02 PDT
