From: Kailee (
Date: Fri May 18 2007 - 10:57:58 CDT

Dear all,

I have been using VMD for visualisation for some time, however I never wrote
any tcl script myself. I have the trajectory file (.mdcrd file) from AMBER
molecular dynamcis calculation that simulated gas diffusion into a protein,
and I have about 300 molecules of the gas molcule diffusing at the same time
into the protein. What I want to do is, I want to know at what time, which
gas molecule (ID) get close to a certain distance to the active site? so for
example, when one gas molecule become within 5 angstrom to the Fe atom in
the active site, the atom ID of that gas molecule and the frame number can
be recorded automatically.

I looked at the VMD script library but couldn't find similar script
available, can I ask has anyone wrote similar script already? or have some
suggestions how to do this? as there might be some better ideas~ any help is
appreciated! Thank you.

Best regards,