[gmx-users] g_dist error

[Justin A. Lemkul]

aiswarya.pawar at gmail.com wrote:
> 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.
> 
> 

As was suggested several messages ago, please do NOT combine -o and -dist.  If 
you want to measure a distance, use -o.  If you want g_dist to print a list of 
atoms that satisfy some given criteria, use -dist, but not together.

-Justin

> Thanks
> Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!
> 
> -----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

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