AMBER Archive (2005)

Subject: AMBER: van der Waals interactions (PTRAJ)

From: Vineet Pande (pande_vineet_at_hotmail.com)
Date: Thu Mar 17 2005 - 08:07:12 CST

Dear AMBER Users & Developers:

In a simulation, I would like to monitor van der Waals interactions between
a Phenylalanine residue and a pyridyl ring which is a part of inhibitor
bound to the protein. Sort of "stacking interactions" are expected >> Does
any one know whats the best way to trap this info, structurally, with
Ptraj....though energetically its facile (with ANAL module).

Thanks,
Vineet

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