Re: mm_pbsa energy unit

From: Holger Gohlke <>
Date: Mon 10 Feb 2003 11:48:51 -0800

Hi Eric,

> Hi, I got a binding energy -55.23+/-6.58. Then I
> calculated the total entropy for the small molecule
> which is 53.46+/-1.17. I want to know the units for
> each case (kcal/mol for binding energy, cal/mol/k for
> entropy?).

The units are in both cases kcal/mol. The values for the entropies and
the solvation free energies in the case of PB calculations (with Delphi)
were calculated for T=300K.

> Also I have another binding energy resulted
> from the same substrate with a different binding mode.
> The binding energy is -54.62+/-5.77. I am not very
> confident to say which mode is energetically better
> since the binding energy difference between the two
> binding modes is within the STD.
> Eric

The quantity which might be more interesting here than the standard
deviation (STD) is the standard error (or uncertainty) in the mean
(SEM). The latter is obtained as SEM = STD / sqrt(N), with N being the
number of INDEPENDENT samples (i.e snapshots). See also "Data reduction
and error analysis for the physical sciences", P. R. Bevington,
McGraw-Hill Book Company.

Best regards


Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla CA 92037  USA
phone: +1-858-784-9788
fax:   +1-858-784-8896
Received on Mon Feb 10 2003 - 11:48:51 PST
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