Hi Gustaf,
thanks for sharing your experience. I successfully compiled and installed
Ambertools 1.2 and Amber10 in my 32 bits machine, fedora 10, following the
same instructions provided in the manual. I am not sure if it is related to
the architecture issue, but from what i have read from the Amber mailing
list, there are people successfully compiled and installed in 64 bits
machine.....
anyway, thanks for your reply.
Thanks and regards,
colvin
On Thu, Jun 10, 2010 at 4:44 PM, Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
> Sorry that I could not be of more assistance.
>
> In my experience, the only thing with amber that has failed me is the
> compiling process.
> There is always a great chance that any error is related to compiler
> problems so you might want to try a different set of compilers.
>
> Hope someone better suited can help you out with this.
>
> Best Regards
> Gustaf
>
> On Jun 10, 2010, at 10:28 AM, colvin wrote:
>
> > Hi Gustaf,
> >
> > Thanks for your reply.
> >
> > FYI, I didn't change anything....
> >
> > Thanks and regards,
> > colvin
> >
> > On Thu, Jun 10, 2010 at 4:18 PM, Gustaf Olsson <gustaf.olsson.lnu.se>
> wrote:
> >
> >> Hi Colvin
> >>
> >> Have you modified your source code in any way?
> >>
> >> I'm no computer wizard but it seems that there is something
> >> wrong/missing/added in some files.
> >>
> >> Best regards
> >> Gustaf
> >>
> >> On Jun 10, 2010, at 9:43 AM, colvin wrote:
> >>
> >>> Dear all,
> >>>
> >>> Good day.
> >>>
> >>> I have been trying to compile and install *ambertools1.2* for
> *amber10*,
> >>> following the instructions in the manual, but i am getting these error
> >>> messages (showing only the last part of the message):
> >>>
> >>> ./nab -c bdna.nab
> >>> ./nab -c dg_helix.nab
> >>> ./nab -c getchivol.nab
> >>> ./nab -c getres.nab
> >>> ./nab -c getseq_from_pdb.nab
> >>> ./nab -c getxyz_from_pdb.nab
> >>> ./nab -c -DBINDIR='"/usr/local/amber10/bin"'
> >>> -DDATDIR='"/usr/local/amber10/dat"' getpdb_prm.nab
> >>> ./nab -c getpdb_rlb.nab
> >>> ./nab -c linkprot.nab
> >>> ./nab -c link_na.nab
> >>> ./nab -c -DDATDIR='"/usr/local/amber10/dat"' na_anal.nab
> >>> na_anal.c:2417:41: warning: missing terminating " character
> >>> na_anal.c: In function helixanal:
> >>> na_anal.c:2417: error: expected ) before is
> >>> na_anal.c:2417: error: stray \ in program
> >>> na_anal.c:2417:40: warning: missing terminating " character
> >>> na_anal.c:2417: error: missing terminating " character
> >>> na_anal.c:2419: error: expected ; before } token
> >>> cc failed!
> >>> make[1]: *** [na_anal.o] Error 1
> >>> make[1]: Leaving directory `/usr/local/amber10/src/nab'
> >>> make: *** [install] Error 2
> >>>
> >>>
> >>>
> >>> i then cd ../test and type make -f Makefile_at test, these messages
> >>> appeared:
> >>>
> >>> ( cd nab; make test )
> >>> make[1]: Entering directory `/usr/local/amber10/test/nab'
> >>> =====================================================
> >>> Running test to make dna duplex:
> >>>
> >>> /bin/sh: /usr/local/amber10/bin/nab: No such file or directory
> >>> /bin/sh: line 1: ./duplex: No such file or directory
> >>> make[1]: *** [duplex_test] Error 127
> >>> make[1]: Leaving directory `/usr/local/amber10/test/nab'
> >>> make: *** [test.nab] Error 2
> >>>
> >>>
> >>>
> >>> This is my *config.h* file:
> >>>
> >>> Setting AMBERHOME to /usr/local/amber10
> >>>
> >>>
> >>> Testing the C compiler:
> >>> gcc -m64 -o testp testp.c
> >>> OK
> >>>
> >>> Obtaining the C++ compiler version:
> >>> g++ -v
> >>> The version is 4.4.3
> >>> OK
> >>>
> >>> Testing the g77 compiler:
> >>> g77 -O2 -fno-automatic -finit-local-zero -o testp testp.f
> >>> OK
> >>>
> >>> Testing flex:
> >>> OK
> >>>
> >>> Configuring netcdf; (may be time-consuming)
> >>>
> >>> NETCDF configure succeeded.
> >>>
> >>> The configuration file, config.h, was successfully created.
> >>>
> >>> The next step is to type 'make -f Makefile_at'
> >>>
> >>>
> >>>
> >>> gcc version: *gcc (GCC) 4.4.3 *20100127 (Red Hat 4.4.3-4)
> >>> system information: *Fedora12, Intel Xeon 64 bits*
> >>>
> >>>
> >>> I need help and advice here. Thanks in advance for your time.
> >>>
> >>> Thanks again.
> >>>
> >>> Regards,
> >>> colvin
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
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> >>
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>
>
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Received on Thu Jun 10 2010 - 02:00:05 PDT
