Again bothering you, the message Amber returned after test passing is
copied here and the log file also attached.
make[3]: Leaving directory
`/home/asma/AAData/AMBER/amber12/AmberTools/test/paramfit'
Finished test suite for AmberTools at Wed May 16 10:23:45 PKT 2012.
make[2]: Leaving directory `/home/asma/AAData/AMBER/amber12/AmberTools/test'
567 file comparisons passed
17 file comparisons failed
1 tests experienced errors
Test log file saved as
/home/asma/AAData/AMBER/amber12//logs/test_at_serial/2012-05-16_09-52-33.log
Test diffs file saved as
/home/asma/AAData/AMBER/amber12//logs/test_at_serial/2012-05-16_09-52-33.diff
make[1]: Leaving directory `/home/asma/AAData/AMBER/amber12/AmberTools/test'
==============================================================
/home/asma/AAData/AMBER/amber12//src/Makefile not found, or -noamber was
set.
This is expected if you have not installed Amber12.
==============================================================
On Wed, May 16, 2012 at 10:09 AM, Asma Abro 28-FBAS/MSBI/F09 <
asma.msbi28.iiu.edu.pk> wrote:
> Sorry I get to know about test passing. Yes it has passed all the tests.
> What else should I check to remove the error I have pasted in the last mail?
>
>
> On Wed, May 16, 2012 at 9:05 AM, Asma Abro 28-FBAS/MSBI/F09 <
> asma.msbi28.iiu.edu.pk> wrote:
>
>> The same error message which I was getting using Amber10, i am getting
>> with Amber12. Yes It has an sqm executable file in $AMBERHOME/bin. How can
>> I check for passing test cases? I am sorry for asking stupid questions but
>> I am new to it so having lots of problems.
>>
>> Full message is pasted here:
>> Running: /home/.../AMBER/amber12/bin/bondtype -j full -i
>> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
>>
>> Running: /home/.../AMBER/amber12/bin/atomtype -i ANTECHAMBER_AC.AC0 -o
>> ANTECHAMBER_AC.AC -p gaff
>> Total number of electrons: 247; net charge: 0
>> INFO: Number of electrons is odd: 247
>> Please check the total charge (-nc flag) and spin multiplicity (-m
>> flag)
>>
>> Running: /home/.../AMBER/amber12/bin/sqm -O -i sqm.in -o sqm.out
>> Error: cannot run "/home/asma/AAData/AMBER/amber12/bin/sqm -O -i sqm.in-o sqm.out" of bcc() in charge.c properly, exit
>>
>>
>>
>> On Tue, May 15, 2012 at 5:59 PM, case <case.biomaps.rutgers.edu> wrote:
>>
>>> On Tue, May 15, 2012, Asma Abro 28-FBAS/MSBI/F09 wrote:
>>> >
>>> > I have installed AmberTools12 in my system and I am running antechamber
>>> > with ambertools12 but I am still getting the error. I have checked the
>>> > Variable too, it is not set to wrong location. Can you please suggest
>>> me
>>> > something I do to remove the error?
>>>
>>> It's hard to be sure what you mean by "the error" you are getting. As I
>>> remember the earlier email, it said that you did not have sqm in
>>> ..../amber10/bin. This would be expected, since sqm was not a part of
>>> Amber10. Now you say you have AmberTools12, are are still getting the
>>> error,
>>> but the error must be different(?).
>>>
>>> Don't be vague! Don't say that "AMBERHOME is correct"; instead tell us
>>> what AMBERHOME really is. Is there an sqm executable in your
>>> $AMBERHOME/bin
>>> directory? Do the antechamber test cases pass? Can you cut and paste
>>> the
>>> *exact* error message?
>>>
>>> ....dac
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>
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Received on Tue May 15 2012 - 23:00:03 PDT
