[Chimera-users] pi-cation interaction

Elaine Meng meng at cgl.ucsf.edu
Thu Feb 9 09:16:59 PST 2012

Hi Bishwajit,
Again, there is no specific tool, you would use the general tool for finding contacts.  Either you would find all contacts and then determine yourself which are pi-cation, or restrict identification to only aromatic rings and cationic atom types.  You would still need to check visually, however, since "contacts" depend only on distance and VDW radii, but not the angle of the interaction.

Example commands:
sel aromatic ring
findclash sel test Ng+|N3+ overlap -1 hb 0 log true

You might want to use different command options, such as saving distances to a file, different cutoff distance, including more cationic atom types, etc.


Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Feb 9, 2012, at 7:45 AM, Bishwajit Das wrote:

> how to find cation pi-interaction in a docked molecule.......plz help me 

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