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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Received on Sun Oct 03 2010 - 11:30:04 PDT
