[gmx-users] g_dist error

[Justin A. Lemkul]

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

========================================