AMBER Archive (2009)

Subject: RE: [AMBER] mm_pbsa-Binding and Stability tests?

From: Niel Henriksen (
Date: Mon Aug 24 2009 - 12:24:09 CDT

>And, can I skip warning messages for (MM_ELE, GB_GBSOL and MM_GAS)
>when calculating binding energy and stability energy?

>From what I can tell (without seeing your input and output), this is just a
problem with the statistics calculations. Depending on the output from
sander, the statistics script can sometimes get confused. You can (and
should) directly check the *.*.all.out files and calculate your own
numbers if you don't trust the statistics output.
By the way, the header above the values that you changed in the file explains what the difference between
1 and 0 is for those calculations.

Lastly, as a disclaimer: If you get errors for an mm_pbsa
calculation that you don't understand, doing the procedure manaully
(creating your own sander input, running it, calculating results) is very
instructive. Good luck.


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