Dear Ray,
After I've taken a look at nmode_lig.1.in file I've seen:
&data
ntx = 0,
ntrun = 1, nvect = 0,
drms = 1,
dielc = 4.0, idiel = 0,
scnb = 2.0, scee = 1.2
&end
END
I think that the problem lies in ntx=0. When I change ntx=0 in ntx=1
everything works very well.
Also I have managed to finish successfully test:MMPBSA_Nmode (like you
said with few numbers not exactly reproduced).
I hope that this is a good way of solving my problem.
All the best,
Antonija
Citiram Ray Luo <ray.luo.uci.edu>:
> 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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Received on Tue Jan 26 2010 - 01:30:03 PST
