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
>>
>>
>> _______________________________________________
>> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 10 2010 - 02:00:03 PDT
