AMBER Archive (2009)

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

From: Niel Henriksen (niel.henriksen_at_utah.edu)
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
mm_pbsa_statistics.pm 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.

--Niel

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