[gmx-users] g_dist error

[aiswarya.pawar at gmail.com]

Even if I specify an atom say 1277 atom number to find distance against the OW atoms. I get the same result of SOL-OW distance. Is it a bug cause even after specifying one atom from a protein why doesn't it give me the result for the SOL.


Thanks
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-----Original Message-----
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Sender: gmx-users-bounces at gromacs.org
Date: Mon, 12 Sep 2011 07:52:54 
To: Discussion list for GROMACS users<gmx-users at gromacs.org>
Reply-To: jalemkul at vt.edu,
	Discussion list for GROMACS users <gmx-users at gromacs.org>
Subject: Re: [gmx-users] g_dist error



aiswarya pawar wrote:
> hi Justin,
> 
> As far i referred the OW,HW1 etc are water atoms so how can it be 
> distance between the SOL protein atoms, instead it is SOL water atoms.
> 

The printed distance indicates that there is a certain water molecule that is 
just over 2 hydrogen bonding lengths away from your protein's backbone.  Sounds 
normal to me.

-Justin

> Thanks
> 
> On Mon, Sep 12, 2011 at 4:49 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     aiswarya pawar wrote:
> 
>         Hi Users,
> 
>         Am using g_dist to find the distance between water and protein.
>         but my output has the values of SOL-water distance.
> 
>         t: 1  136 SOL 2336 OW  0.772373 (nm)
> 
> 
>     This is not a water-water distance, it is the output of the -dist
>     option telling you that water molecule 136 has its OW atom at
>     0.7723273 nm from whatever your reference group is.
> 
>     -Justin
> 
>     -- 
>     ==============================__==========
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>     <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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