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Maybe someone here is familiar with supramolecules calculations using Spartan? I am new in this area and trying to figure out some things: First - what's the best way to draw them? I tried to draw one molecule and then using copy-paste append the others but then they overlap and it takes forever to minimize their energy so they make hydrogen bonds in the places I need. Maybe there is any way to 'freeze' hydrogen bonds? Because I now where they shoud be (or at least want to calculate different structures with hb in different places of molecules). If I try to put this molecules near when sketching still when I try to minimize the energy hb forms not in the exact places I need them to be. And I need four molecules to form kinda cyclic-structure. Thank you in advance!

hb I need between two molecules are: enter image description here

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You can create distance constraints between two atoms (set them to the distance you expect for the hydrogen bonds), and then do a force field minimisation.

It's in the menu called Geometry, and then "Constrain distance". You pick the atoms, and click the little lock in the lower right-hand corner, and then enter the distance you want next to the lock.

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  • $\begingroup$ Thank you! But if I don't know what should be the distance? How I could calculate it first? $\endgroup$ – cinnamon May 29 '16 at 12:17
  • $\begingroup$ I would just use a typical value (1.6-2.0 Å, Wikipedia) as a first approximation. Then after you get the geometry in the ballpark, you can remove the constraints and do a more accurate minimisation. $\endgroup$ – Brian May 30 '16 at 13:49

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