AMBER Archive (2007)

Subject: AMBER: Ligand-Residue interaction tracking

From: Evan Kelly (ebkelly_at_ualberta.ca)
Date: Mon Dec 10 2007 - 12:20:29 CST

Hi Everyone,

I have done a simulation of a drug ligand bound to a protein. I was
hoping to analyze the interactions between certain important
functional groups on the drug and the protein. I had envisioned
monitoring the distances between the functional groups and the protein
residues, similar to what the HBOND facility does in ptraj. The
result would be a list of residues (or atoms of residues) that the
functional group is near and for how much of the simulation. I am
unsure of how to best do this. Can anyone offer a suggestion?

Thanks!

----------------------------------
Evan Kelly
ebkelly_at_ualberta.ca

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