Hi AMBER users,
I managed to use MMPBSA to calculate the binding free energy between a small
DNA molecule and an anti-DNA antibody. I also tried to calculate the entropy
with normal mode analysis. However, none of these calculations finished
normally. In a lot of cases, I got such none-sense numbers:
"Entropy Term Average Std. Dev.
------------------------------
-----------------------------
Translational: -1.0000 0.0000
Rotational: -1.0000 0.0000
Vibrational: -1.0000 0.0000
Total: -1.0000 0.0000
DELTA S total= 1.0000 +/- 0.0000
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
WARNINGS:
Not all of your snapshots minimized within tolerable limits for nmode"
And in the log.error file , "Warning: Not all of your snapshots minimized
within tolerable limits for nmode" showed up again.
Is it a memory issue? If not, how could I fix this problem?
Yi An
Graduate student
Department of Chemistry
Texas A&M University
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Received on Fri Apr 29 2011 - 13:30:05 PDT
