AMBER: using hydrogen bond facility to monitor ion pair interaction

From: Zhenwei Lu <>
Date: Thu, 10 Jan 2008 12:09:09 -0500

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.OD1
donor mask :95.OD2
donor mask :97.OD1
donor mask :97.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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Received on Sun Jan 13 2008 - 06:07:14 PST
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