VMD-L Mailing List

From: Kailee (kaileeamber_at_googlemail.com)
Date: Mon Jun 11 2007 - 12:10:30 CDT

Dear all,

I want to analyse a trajectory file from AMBER (.mdcrd), which is a MD
simulation of some gas molecules diffusing into a protein. Is there any way
to calculate the number of times each protein atom collides with the gas
molecules, and then store the number of collisions for each protein atom in
the B-factor of the PDB file so that I can visualise the structure in VMD?

Thank you for any suggestions.

Best regards,
Kailee