AMBER Archive (2008)

Subject: Re: AMBER: ptraj, hbond and non-bonded contacts

From: Thomas Cheatham III (
Date: Thu Mar 13 2008 - 12:49:14 CDT

> 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

The best solution is to specify the heavy atom twice; this ignores the
angle so you simply get the contacts.

acceptor ALA CB CB

-- tec3
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