AMBER Archive (2008)

Subject: Re: AMBER: using hydrogen bond facility to monitor ion pair interaction

From: Thomas Cheatham III (
Date: Thu Jan 10 2008 - 11:21:10 CST

> I tried to monitor MG coordination in the MD trajectory using Hydrogen bond
> faclity. it is known that MG coordinate with two carboxyl group of two ASPs.
> here is the input file I use:
> trajin md2.mdcrd 1 100
> center :1-200
> image familiar
> strip ~:1-200
> donor mask :95_at_OD1
> donor mask :95_at_OD2
> donor mask :97_at_OD1
> donor mask :97_at_OD2
> acceptor MG MG MG
> hbond distance 5 angle 0

First off, do the MG ions ever get closer than 5 angstroms? Have you
looked at the radial distribution function for MG with those oxygens to
see how close the approach is? The hbond will not trigger an interaction
unless it is less than 5 A; I would change this to something smaller, like
3.5A but better would be somewhat shorter than the first peak in the RDF.

Also, to the hbond command I would add more keywords to provide more

hbond series hb out hbond.dat \
  distance 3.5 angle -1.0

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