Something wrong with the nmode program. Can you pass the test under
$AMBERHOME/test/nmode? What's in your nmode output file "nmode_lig.1.out"?
All the best,
Ray
==========================================
Ray Luo, Ph.D.
Associate Professor in Computational
Biochemistry and Molecular Biophysics
Dept of Molecular Biology and Biochemistry
Dept of Biomedical Engineering
University of California, Irvine, CA 92697-3900
Email: rluo.uci.edu Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/rayl/
==========================================
Antonija Tomić wrote:
>
> I must admit that my problem isn't exact reproducing numbers after
> test:MMPBSA_Nmode because I have never come to an end of the
> calculations, i.e. when I type:
>
> /usr/local/amber10/exe/mm_pbsa.pl mm_pbsa.in > mm_pbsa.log
>
> in the /usr/local/amber10/src/mm_pbsa/Examples/04_MMPBSA_Nmode folder
> I get the following message:
>
> /usr/local/amber10/exe/nmode -O -i nmode_lig.in -o -c
> sanmin_lig.1.restrt -p ../raf_wt.prmtop not running properly
>
>
> Maybe this is the reason why I get the following message after typing
> $make test.MMPBSA_Nmode:
>
> make: *** [test.MMPBSA_Nmode] Error 25
>
> I get exact message ("not running properly") when I try to do
> MMPBSA_Nmode calculations with my ligand.
>
> King regards,
> Antonija
>
>
>
>
>
> Citiram "Ray Luo, Ph.D." <ray.luo.uci.edu>:
>
>> Indeed, a few nmode numbers cannot be exactly reproduced in
>> test.MMPBSA_Nmode due to a change in the nmode program. This is a normal
>> behavior.
>>
>> All the best,
>> Ray
>>
>> 2010/1/22 Antonija Tomić <Antonija.Tomic.irb.hr>
>>
>>> Dear Amber Users,
>>>
>>> I must admit I am a part of Amber community who still has problems with
>>> mm_pbsa.
>>> MMPBSA Stability, Binding, ... is working very well, but when I try
>>> to do:
>>>
>>> $make test.MMPBSA_Nmode
>>>
>>> I get the following message.
>>>
>>> cd 04_MMPBSA_Nmode/; /usr/local/amber10/exe/mm_pbsa.pl mm_pbsa.in >
>>> mm_pbsa.log 2>&1
>>>
>>> make: *** [test.MMPBSA_Nmode] Error 25
>>>
>>>
>>> I am wondering if someone has encounter the same problem? Any
>>> suggestions
>>> how to solve it?
>>> I tried to find the solution on google but I failed.
>>>
>>> Kind regards,
>>> Antonija
>>>
>>>
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>>>
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>
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Received on Mon Jan 25 2010 - 11:00:02 PST
