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
Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034
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 .