[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
Re: [modeller_usage] objective function
- To: Gianluca Croce <gianluca.croce AT mfn.unipmn.it>
- Subject: Re: [modeller_usage] objective function
- From: Modeller Caretaker <modeller-care@ucsf.edu>
- Date: Mon, 17 May 2004 10:05:21 -0700
- Cc: modeller_usage@listsrv.ucsf.edu
On Mon, May 17, 2004 at 09:40:53AM +0200, Gianluca Croce wrote:
> I'm a new user of modeller and I would like to know
> which it is the measure unit used from mod6v2 for the
> objective function? It is possible to have a correlation
> between the unit of objective function and other units
> (Kcal/mol, KJ/mol etc)?
The parameters and topologies used by Modeller for calculating the
objective function are CHARMM files, so the energy is nominally in
kcal/mol. However, the energy is strongly dependent on your choice of
restraints, and should at best be considered a 'pseudo energy'; for
example, it's probably unwise to directly compare the energies of two
different proteins.
Ben Webb, Modeller Caretaker
--
modeller-care@ucsf.edu http://www.salilab.org/modeller/
Modeller mailing list: http://salilab.org/mailman/listinfo/modeller_usage