AMBER Archive (2008)

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

From: Zhenwei Lu (
Date: Thu Jan 10 2008 - 11:09:09 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

However, nothing comes out. From the output of ptraj, both donors and
acceptors are correctly identified.

So I hope anyone can give me some help about this.


Zhenwei Lu
Graduate Student
Biochemistry & Molecular Biology
313 Biochemistry building
Tel: 517-353-8786

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