I analyzed the .out files of mm_pbsa.pl script and compared them with the
.statistics.out file. It seems that all the values in .statistics.out
calculated with mm_pbsa.pl script is in kcal/mol (entropy, pbsa, gbsa,
vacuum). In the amber mailing list, there were similar questions regarding
the units of the outputs of mm_pbsa.pl script. It looks like that people
also got confused with the units.
I think that it might be a good thing to include this information
explicitly in the manual. nmode's units are in cal/mol-K, while the
mm_pbsa.pl script's outputs are all in kcal/mol (entropic part is T*S
where T=300K). mm_pbsa.pl script also spits out the energy information for
complex/ligand/receptor (.com.all.out, .lig.all.out, .rec.all.out), and
in order to use those files for some other calculations (such as
convergence analysis), it is important to know the units. In any case,
just a suggestion.
Best,
On Fri, 12 Dec 2008, David A. Case wrote:
> On Thu, Dec 11, 2008, Ilyas Yildirim wrote:
> >
> > "the si system of units is used internally. conversion to units more
> > familiar to most chemists is made for output."
>
> "more familiar to most chemists" means cal/mol-deg for entropy.
> Furthermore, the output is very clear (unusual for Amber!), with lines like
> this:
>
> freq. E Cv S
> cm**-1 kcal/mol cal/mol-kelvin cal/mol-kelvin
> --------------------------------------------------------------------------------
> Total 45.379 32.658 99.218
> translational 0.888 2.979 40.781
> rotational 0.888 2.979 29.811
> vibrational 43.603 26.700 28.627
>
> ...dac
>
>
--
Ilyas Yildirim, Ph.D.
---------------------------------------------------------------
= Hutchison Hall B#10 - Department of Chemistry =
= - University of Rochester =
= 585-275-6766 (office) - =
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Received on Sun Dec 14 2008 - 01:13:22 PST
