Hi Thomas,

I would suggest the maximum distance for this "aromatic" pi stacking interaction would be 4 angstrom. As for the constraints...not sure on the how to

_________________________________ Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall http://www.researcherid.com/rid/C-2803-2008 Pukeka Matua Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 56 Otepoti 9054 Aotearoa

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From: modeller_usage-bounces@salilab.org [mailto:modeller_usage-bounces@salilab.org] On Behalf Of Thomas Evangelidis Sent: Saturday, 27 February 2010 3:47 p.m. To: modeller_usage@salilab.org Subject: Re: [modeller_usage] special restrains for aromatic packing interactions

Dear Modellers,

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:

http://personalpages.manchester.ac.uk/postgrad/Thomas.Evangelidis/aromatic_p...

I have labelled the atoms to help you. I'm wondering what would be the best stereochemical restrains to describe this interaction? A list with Modeller's stereochemical restrains can be found here:

http://salilab.org/modeller/manual/node196.html

Or would an Energy-based restrain describe that interactions better? Any suggestions are welcome.

thanks, Tom

By the way, what should be the maximum distance of electrostatic interactions. Usually the maximum distance between H-bond donor and acceptor is set to 3.2 A. (although sometimes may be 3.5 A.), but considering the resolution of crystal structures shouldn't it be a bit longer? Also in the tutorial is set to 3.5+-0.1 .

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 >