[ghemical-devel] MM/QM: assumptions

[Parker Jones]

Thanks for the helpful response, Tommi.  It appears I have been violating 
the assumptions for MM calculations.  I'd like to calculate the energy of 
the LHS and RHS of a reaction where substrates and products are small 
metabolites.  You mention that QM energies are comparable in some cases.   
In that case, can one simply sum the QM energies of the molecules of each 
side?  Any pointers to the assumptions of QM calculations would be much 
appreciated.

Best,

Parker J.




>From: Tommi Hassinen <thassine@messi.uku.fi>
>To: Parker Jones <zoubidoo@hotmail.com>
>CC: ghemical-devel@bioinformatics.org
>Subject: Re: [ghemical-devel] MM: geometry optimisation gives negative 
>energy???
>Date: Mon, 23 Aug 2004 10:15:00 +0300 (WET)
>
>On Sun, 22 Aug 2004, Parker Jones wrote:
>
> > Dear All,
> >
> > I am doing geometry optimisation of a small metabolite and end up with a
> > minimum of  Energy = -2.19629109 kJ/mol.  All my other calculations have
> > given positive energies, so I am a little surprised.
> >
> > Is this a valid result or could it be a bug?
>
>Hello,
>
>a single MM energy calculated for a single conformer really does not
>contain any information ; you only can compare energies calculated for
>different conformations for a molecule/compound, and since you only can
>compare the energies the zero-level is not important (and usually it is
>arbitrary in mol.mech. force fields).
>
>The MM energies calculated for different molecules/compounds are not
>comparable.
>
>The QM energies are comparable in some cases ; for example when both
>compounds have the same composition (like ethanol CH3CH2OH and
>dimethylether CH3OCH3) you should be able to compare their stability from
>energy results calculated using identical methods. But I'm not really an
>expert of this topic.
>
>Regards,
>
>	Tommi
>

_________________________________________________________________
Listen to music online with the Xtra Broadband Channel  
http://xtra.co.nz/broadband