Hi all, 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)? Regards, G. -- Gianluca Croce Ph. D. Student DISTA- Universita' del Piemonte Orientale C.so T. Borsalino 54, Alessandria I-15100 Italy Tel_office: +39 0131 287414 Fax: +39 0131 287416 visit my Web page at the URL: www.mfn.unipmn.it/~gcroce
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@salilab.org http://www.salilab.org/modeller/ Modeller mailing list: http://salilab.org/mailman/listinfo/modeller_usage
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Gianluca Croce -
Modeller Caretaker