AMBER Archive (2009)

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

From: Antonija Tomić (Antonija.Tomic_at_irb.hr)
Date: Mon Aug 24 2009 - 04:51:28 CDT

Hi

I followed the link ( http://archive.ambermd.org/200806/0357.html )
and edited my mm_pbsa_statistics.pm (by changing 1 of ELRAELE, EPB,
PBNONPOL to 0). No longer I have errors like:

WARNING: Missing PBNONPOL for PB in 0 -> Taken from -1
WARNING: Missing ELRAELE for PB in 0 -> Taken from -1
WARNING: Missing EPB for PB in 0 -> Taken from -1
.
.
.

BUT I STILL HAVE:

No values for MM_ELE existing -> Skipping
No values for GB_GBSOL existing -> Skipping
No values for MM_GAS existing -> Skipping

My first question is the same as in the link above:
Can anyone tell me if this was a valid way of solving the
problem or have I misunderstood something?
And, can I skip warning messages for (MM_ELE, GB_GBSOL and MM_GAS)
when calculating binding energy and stability energy?

Grateful
Antonija

Citiram Niel Henriksen <niel.henriksen_at_utah.edu>:

>
>> Reading ras_raf_II_wt_com.all.out
>> WARNING: Missing PBNONPOL for PB in 0 -> Taken from -1
>> WARNING: Missing ELRAELE for PB in 0 -> Taken from -1
>> WARNING: Missing EPB for PB in 0 -> Taken from -1
>
> The following post may describe a fix for your problem:
>
> http://archive.ambermd.org/200806/0357.html
>
> --Niel
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