Re: [modeller_usage] special restrains for aromatic packing interactions

[Modeller Caretaker <modeller-care@ucsf.edu>]

On 3/24/10 10:36 AM, Thomas Evangelidis wrote:
> Is it possible to set the distance cutoff between a given atom of the
> protein and a subset of atoms in the ligand?

Sure, you can create a pseudoatom which is some function of the subset, 
e.g. the gravity center, and then create a distance restraint between 
the given atom and your newly-created pseudoatom. One example is at
http://salilab.org/modeller/wiki/Restraints%20on%20pseudo%20atoms

> E.g. in some crystal
> structures OG1 of a THR forms an H-bond with O1A of ATP, whereas in
> others with O2A. In that case can I force Modeller to keep (THR44:OG1 -
> ATP266:O1A <= 3.5+-0.1) OR (THR44:OG1 - ATP266:O2A <= 3.5+-0.1)  ?

You could use features.minimal_distance for this rather than the regular 
features.distance:
http://salilab.org/modeller/9v7/manual/node97.html#SECTION001031200000000000000

	Ben Webb, Modeller Caretaker
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