AMBER Archive (2008)

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

From: Zhenwei Lu (luzhenw1_at_msu.edu)
Date: Thu Jan 10 2008 - 12:16:57 CST

I got it. the key point is setting the angle cut-off to -1. Thanks a lot.

 

Thomas Cheatham III writes:

>
>> 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
> information...
>
> hbond series hb out hbond.dat \
> distance 3.5 angle -1.0
>
> --tec3
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Zhenwei Lu
Graduate Student
Biochemistry & Molecular Biology
313 Biochemistry building
Tel: 517-353-8786
Email: luzhenw1_at_msu.edu

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