Hi,
These small errors appear to be mainly due to rounding. I would say they are
probably small enough that the warning message can be ignored.
-Bill
On Sun, Oct 3, 2010 at 2:12 PM, William Flak <williamflak.yahoo.com> wrote:
> Dear AMBER
> In MMPBSA output, I got the following warning:
>
> WARNING: INCONSISTENCIES EXIST WITHIN INTERNAL POTENTIAL TERMS (BOND,
> ANGLE, AND/OR DIHED).
> CHECK YOUR INPUT FILES AND SYSTEM SETUP. THESE RESULTS MAY NOT BE RELIABLE
> (check differences)!
> Common causes include improperly used initial_traj variable or improperly
> set masks.
>
> According to a previous post regarding to the same warning I found you
> recommended to check the difference section in the output (
> http://archive.ambermd.org/201008/0388.html)
> As I see, the differences are nearly zero in all my outputs and my binding
> energy values are ranging between 15 and 30 kcal/mol
>
> Differences (Complex - Receptor - Ligand):
> Energy Component Average Std. Dev. Std. Err. of
> Mean
>
> -------------------------------------------------------------------------------
> BOND -0.0000 0.0001 0.0000
> ANGLE 0.0000 0.0001 0.0000
> DIHED -0.0025 0.0075 0.0008
> VDWAALS -34.5452 1.8611 0.1861
> EEL 1.0172 2.3867 0.2387
> EPB 19.5129 4.1644 0.4164
> ECAVITY -1.9062 0.0728 0.0073
>
> so, should I ignore this warning? or there is something should I check?
> By the way, I use mmpbsa.py for mmpbsa calculation
> Thanks in advance;
> W. Flak
>
>
>
>
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>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Sun Oct 03 2010 - 11:30:05 PDT
