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 nmode_lig.1.out -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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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Mon Jan 25 2010 - 02:30:02 PST
