Thanks Bill for this information.
On 7/10/14, Bill Miller III <brmilleriii.gmail.com> wrote:
> This warning message is printed because your internal energy terms (BOND,
> ANGLE, DIHEDRALS) do not sum to zero for the DELTA energies. This can be
> indicative of several different issues. However, looking at your output
> file, those terms are all very near zero:
>
> BOND -0.0000
> ANGLE 0.0000
> DIHED 0.0003
>
> Those are close enough to zero still that I would say there are no serious
> problems with your system or calculation that are being flagged by this
> message.
>
> Good luck!
>
> -Bill
>
>
> On Thu, Jul 10, 2014 at 8:58 AM, Him Shweta <shwetahim.gmail.com> wrote:
>
>> dear all,
>>
>> I am calculating binding free energy using MMPBSA.py for
>> quadruplex-ligand system using the below given input file:
>> Input file for running PB and GB in serial
>>
>> |&general
>>
>> | endframe=100, interval=1, keep_files=0, strip_mask=:WAT, Na+,
>>
>> |/
>>
>> |&gb
>>
>> | igb=2,
>> |/
>>
>> |&pb
>>
>> | istrng=0.000, exdi=80, indi=1.0,
>> | inp=1, cavity_surften=0.00542, cavity_offset=0.92,
>> | fillratio=4, scale=2.0, prbrad=1.4, radiopt=0,
>>
>> |/
>>
>>
>> All calculation went well. But when i checked the output file, a
>> warning was printed
>> "WARNING: INCONSISTENCIES EXIST WITHIN INTERNAL POTENTIAL
>> TERMS. THE VALIDITY OF THESE RESULTS ARE HIGHLY QUESTIONABLE"
>>
>> I want to know that is there any serious problem with the result or
>> its just a warning. The output file is attached here.
>>
>> Looking forward for your responce and suggestions.
>>
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>>
>>
>
>
> --
> Bill Miller III
> Post-doc
> University of Richmond
> 417-549-0952
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>
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Received on Thu Jul 10 2014 - 06:30:02 PDT
