Thanks for reply
Actually I have 2ns trajectroy and I am doing MMPBSA nomde in parts.
For 1-500ps it gave warning
WARNINGS:
Not all of your snapshots minimized within tolerable limits for nmode
But for 501-1000ns didnt gave any warning
DELTA S total= -54.4966 +/- 25.8445 (for 1-500ps)
DELTA S total= -53.9573 +/- 19.4499 (for 501-1000ps)
So I think It may me memmory issue.
As you have suggested to increase maxcyc but I am using MMPBSA.py so how I can
increase
maxcyc?
> I would say that despite you actually getting entropy results in the output
> file, I would not put a lot of stock into the reliability of those results
> if some of the snapshots did not properly minimize. I would suggest
> increasing the maxcyc in the input file to improve your chances of
> successfully minimizing all your snapshots.
>
> -Bill
>
> On Sat, May 28, 2011 at 12:45 PM, Sangita Kachhap <sangita.imtech.res.in>wrote:
>
>> Thanks for reply
>>
>> I have got entropic result this warning is written at the end of output
>> file.
>>
>> Here I am attaching energy output file.
>>
>>
>> > My guess is since you got this warning message that you did not get any
>> > entropic results with your calculation, is that correct? In that case,
>> you
>> > will need to fix this problem in order to get your final results.
>> >
>> > -Bill
>> >
>> > On Sat, May 28, 2011 at 5:41 AM, Sangita Kachhap <sangita.imtech.res.in
>> >wrote:
>> >
>> >>
>> >> Hello All
>> >>
>> >> I am doing MMPBSA nmode analysis. Job has completed successfully but
>> with a
>> >> warning.
>> >>
>> >> WARNINGS:
>> >> Not all of your snapshots minimized within tolerable limits for nmode
>> >>
>> >> Will it affect my final result?
>> >>
>> >> With regard
>> >>
>> >> 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
>>
>> _______________________________________________
>> 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 Tue May 31 2011 - 09:30:03 PDT
