With respect to my second question, how long do you advice me to set the distance between 2 atoms that are supposed to form an H-bond?
2010/3/2 Modeller Caretaker modeller-care@salilab.org
> On 2/26/10 5:32 AM, Thomas Evangelidis wrote: > >> I'm trying to apply restrains to the interactions of cavity residues >> with ATP. Apart from electrostatic interactions between atom pairs, a >> Tyr residue is always packed parallel with the Adenine ring of ATP, as >> shown in this pic: >> > > To model this, you'd need to add one or more additional restraints: > http://salilab.org/modeller/9v7/manual/node204.html > > I'm not sure what the best form would be for a pi-stacking interaction. For > stacking of two 6-membered rings, with Modeller restraints you could add 6 > distance restraints between the pairs of atoms (but that would prevent > rotation, of course) or create two centers of gravity, one for each ring, > and add a single distance restraint between the two (but that would not > force the rings to lie in the same plane - you'd have to add a few dihedral > restraints to do that). If you can't achieve it with Modeller restraints, > you can certainly write your own. > > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage >