I am doing in 9 cpu workstation.
Input files :
nmod_lig.in
File generated by mm_pbsa.pl
&data
ntrun = 1, nvect = 0,
drms = 1,
dielc = 4.0, idiel = 0,
scnb = 2.0, scee = 1.2
&end
END
sanmin_lig.in
File generated by mm_pbsa.pl
&cntrl
ntf = 1, ntb = 0,
dielc = 4,
cut = 99.0, nsnb = 99999,
scnb = 2.0, scee = 1.2,
imin = 1, maxcyc = 1000,
ncyc = 0, drms = 0.1
&end
&ewald
eedmeth= 5,
&end
> How much memory is available for the calculation? Nmode calculations can be
> very memory intensive for biological systems. What does your input file look
> like?
>
> -Bill
>
> On Sat, Sep 4, 2010 at 7:41 AM, Sangita Kachhap <sangita.imtech.res.in>wrote:
>
>>
>> Hello all
>>
>> I am doing mm_pbsa analysis using amber10 I did the snapshot generation,
>> stability and binding
>> energy calculation successefully but when I am doing nmode analysis getting
>> following
>> error :
>>
>> /home/sangita/amber10/exe/sander -O -i sanmin_lig.in -o sanmin_lig.2.out
>> -c
>> ../snapshot_ras/ras_raf_lig.crd.2 -p ../raf.prmtop -r sanmin_lig.2.restrt
>> not
>> running properly
>>
>> can anybody please suggest me what is the problem?
>>
>> Sangita Kachhap
>> JRF
>> BIC,IMTECH
>> CHANDIGARH
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Bill Miller III
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-6715
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Sat Sep 04 2010 - 05:30:03 PDT
