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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Received on Thu Jul 10 2014 - 06:30:02 PDT
