Thanks Jason,
Indeed, and then I tried to follow the instructions. I am doing a clean
install, but when I do:
cd $AMBERHOME
cd ../
wget
http://ambermd.org/bugfixes/11.0/apply_bugfix.x
wget
http://ambermd.org/bugfixes/11.0/bugfix.all.tar.bz2
chmod +x apply_bugfix.x
./apply_bugfix.x ./bugfix.all.tar.bz2
is this patch applying for AmberTools as well?
I already see some patches not working well. I see:
patching file AmberTools/src/configure
Hunk #1 FAILED at 19.
Hunk #2 FAILED at 369.
Hunk #3 FAILED at 495.
Hunk #4 FAILED at 629.
Hunk #5 FAILED at 642.
Hunk #6 FAILED at 654.
Hunk #7 FAILED at 986.
Hunk #8 FAILED at 1018.
Hunk #9 FAILED at 1055.
Hunk #10 FAILED at 1309.
Hunk #11 FAILED at 1343.
Hunk #12 FAILED at 1497.
Hunk #13 FAILED at 1551.
13 out of 13 hunks FAILED -- saving rejects to file
AmberTools/src/configure.rej
Anyway, I applied
cd $AMBERHOME
wget
http://ambermd.org/bugfixes/11.0/bugfix.18
patch -p0 -N < bugfix.18
as well.
Then, I have to edit configure, I am using gcc-4 (from Fink)
gcc-4 -v
Using built-in specs.
COLLECT_GCC=gcc-4
COLLECT_LTO_WRAPPER=/sw/lib/gcc4.8/libexec/gcc/x86_64-apple-darwin12.3.0/4.8.1/lto-wrapper
Target: x86_64-apple-darwin12.3.0
Configured with: ../gcc-4.8.1/configure --prefix=/sw
--prefix=/sw/lib/gcc4.8 --mandir=/sw/share/man
--infodir=/sw/lib/gcc4.8/info
--enable-languages=c,c++,fortran,lto,objc,obj-c++,java --with-gmp=/sw
--with-libiconv-prefix=/sw --with-isl=/sw --with-cloog=/sw --with-mpc=/sw
--with-system-zlib --enable-checking=release
--x-includes=/usr/X11R6/include --x-libraries=/usr/X11R6/lib
--program-suffix=-fsf-4.8
Thread model: posix
gcc version 4.8.1 (GCC)
I do
cd $AMBERHOME/AmberTools/src
./configure -macAccelerate -nopython gnu
make install
and I got that:
14 warnings generated.
gfortran -c -O3 -mtune=generic -ffree-form -o qm2_dftb_scf.SQM.o
_qm2_dftb_scf.SQM.f
cpp -traditional -P -DBINTRAJ qm2_allocate_e_repul.f >
_qm2_allocate_e_repul.f
gfortran -c -O3 -mtune=generic -ffree-form -o qm2_allocate_e_repul.o
_qm2_allocate_e_repul.f
_qm2_allocate_e_repul.f:42.2:
REQUIRE ( ier == 0 )
1
Error: Unclassifiable statement at (1)
_qm2_allocate_e_repul.f:58.5:
REQUIRE ( ier == 0 )
1
Error: Unclassifiable statement at (1)
make[1]: *** [qm2_allocate_e_repul.o] Error 1
make: *** [serial] Error 2
Any ideas?
Many thanks in advance,
Alan
On 11 October 2013 16:45, Jason Swails <jason.swails.gmail.com> wrote:
> On Fri, Oct 11, 2013 at 11:07 AM, Alan <alanwilter.gmail.com> wrote:
>
> > Hi there,
> >
> > I have Amber11 but I am clueless if I can install it with AmberTools13.
> >
> > If possible, is there a "how-to" for that?
> >
>
> http://jswails.wikidot.com/installing-ambertools-13-and-older-amber
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral ResearcherAMBER Mailing List <amber.ambermd.org>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Alan Wilter SOUSA da SILVA, DSc
Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588
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Received on Fri Oct 11 2013 - 09:30:05 PDT
