AMBER Archive (2008)

Subject: AMBER: ptraj and non-bonded contacts

From: Samuel Genheden (a03samge) (
Date: Wed Mar 12 2008 - 11:34:44 CDT

Hello, Amber users
I've have modelled a protein complex using a docking algorithm and now I'm performing an MD simulation of the docked complex. From the docking algorithm I have got a list of possible hydrogen bonds and a list of possible non-bonded contacts (carbon-carbon interactions). Now I want to track these contacts during the MD simulation...
For the hydrogen contacts it is easy, I just use ptraj and the hbond facilities and it works fine.
But how about the non-bonded contacts. Is it possible to use the hbond facility even for these contacts? As I see is the only problem how to define the acceptor atom. The acceptor command requires an hydrogen and the heavy atom which it is bonded to. Now I have carbons contacts that I want to keep track of, so which bonded atom should I use? My idea is just to take the heavy atom previous in the chain, e.g. a CB for a CG and CA for the CB. Is this a plausible solution?
Best regards, Samuel

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