AMBER Archive (2007)

Subject: AMBER: how is the standard deviations calculated in mm-pbsa?

From: Magne Olufsen (Magne.Olufsen_at_chem.uit.no)
Date: Tue Mar 06 2007 - 06:58:17 CST

Hi AMBER comunity!

I got low standard deviations from complex, receptor and ligand
(percentages). But when the difference between these three
contributions is added in the mm-pbsa script when I perform normal
mode anaysis I got very high standard deviations. Does anyone know
how the standard deviations in the sum is computed?

See the mm-pbsa outbut below

Greetings from Magne Olufsen

# COMPLEX RECEPTOR
LIGAND
# ----------------------- -----------------------
-----------------------
# MEAN STD MEAN STD
MEAN STD
# ======================= =======================
=======================
TSTRA 17.04 0.00 16.86 0.00
15.52 0.00
TSROT 17.55 0.02 17.21 0.01
15.22 0.04
TSVIB 2947.00 17.51 2493.72 14.26
481.47 5.67
TSTOT 2981.60 17.52 2527.79 14.26
512.21 5.69

# DELTA
# -----------------------
# MEAN STD
# =======================
TSTRA -15.34 0.00
TSROT -14.87 0.03
TSVIB -28.19 21.59
TSTOT -58.41 21.60

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