AMBER Archive (2009)

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

From: Antonija Tomić (Antonija.Tomic_at_irb.hr)
Date: Wed Aug 26 2009 - 04:15:54 CDT

Hi,

thank you very much for your help.
After I have calculated things manually I understand it much more better.

Antonija

Citiram Niel Henriksen <niel.henriksen_at_utah.edu>:

>
>> 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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