On 13/09/2011 2:27 PM, aiswarya.pa...@gmail.com wrote:
Iam -dist option because I need the distance between two groups
That is not what g_dist -dist does. Please read g_dist -h.
excluding -dist gives me X,Y,Z output which I don't want.
And other output which you do, but you have to use -o to get it. Read
g_dist -h.
And am not specifying an -o.
You need to specify -o to achieve your purpose. However, as I said quite
a while ago, there is no value in measuring the distance between a
protein phase and a water phase if they are in contact...
Mark
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-----Original Message-----
From: "Justin A. Lemkul"<jalem...@vt.edu>
Date: Mon, 12 Sep 2011 22:35:28
To:<aiswarya.pa...@gmail.com>; Discussion list for GROMACS
users<gmx-users@gromacs.org>
Reply-To: jalem...@vt.edu
Subject: Re: [gmx-users] g_dist error
aiswarya.pa...@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"<jalem...@vt.edu>
Sender: gmx-users-boun...@gromacs.org
Date: Mon, 12 Sep 2011 07:52:54
To: Discussion list for GROMACS users<gmx-users@gromacs.org>
Reply-To: jalem...@vt.edu,
Discussion list for GROMACS users<gmx-users@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<jalem...@vt.edu
<mailto:jalem...@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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