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On 13/09/2011 2:27 PM, <a class="moz-txt-link-abbreviated" href="mailto:aiswarya.pawar@gmail.com">aiswarya.pawar@gmail.com</a> wrote:
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cite="mid:%20%3C1590492281-1315888041-cardhu_decombobulator_blackberry.rim.net-869464651-@b18.c3.bise7.blackberry"
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<pre wrap="">Iam -dist option because I need the distance between two groups</pre>
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<br>
That is not what g_dist -dist does. Please read g_dist -h.<br>
<br>
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<pre wrap=""> excluding -dist gives me X,Y,Z output which I don't want.</pre>
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<br>
And other output which you do, but you have to use -o to get it.
Read g_dist -h.<br>
<br>
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<pre wrap=""> And am not specifying an -o.</pre>
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<br>
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...<br>
<br>
Mark<br>
<br>
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<pre wrap="">
Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!
-----Original Message-----
From: "Justin A. Lemkul" <a class="moz-txt-link-rfc2396E" href="mailto:jalemkul@vt.edu"><jalemkul@vt.edu></a>
Date: Mon, 12 Sep 2011 22:35:28
To: <a class="moz-txt-link-rfc2396E" href="mailto:aiswarya.pawar@gmail.com"><aiswarya.pawar@gmail.com></a>; Discussion list for GROMACS users<a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a>
Reply-To: <a class="moz-txt-link-abbreviated" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>
Subject: Re: [gmx-users] g_dist error
<a class="moz-txt-link-abbreviated" href="mailto:aiswarya.pawar@gmail.com">aiswarya.pawar@gmail.com</a> wrote:
</pre>
<blockquote type="cite">
<pre wrap="">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.
</pre>
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<pre wrap="">
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
</pre>
<blockquote type="cite">
<pre wrap="">Thanks
Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!
-----Original Message-----
From: "Justin A. Lemkul" <a class="moz-txt-link-rfc2396E" href="mailto:jalemkul@vt.edu"><jalemkul@vt.edu></a>
Sender: <a class="moz-txt-link-abbreviated" href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a>
Date: Mon, 12 Sep 2011 07:52:54
To: Discussion list for GROMACS users<a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a>
Reply-To: <a class="moz-txt-link-abbreviated" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>,
Discussion list for GROMACS users <a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a>
Subject: Re: [gmx-users] g_dist error
aiswarya pawar wrote:
</pre>
<blockquote type="cite">
<pre wrap="">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.
</pre>
</blockquote>
<pre wrap="">
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
</pre>
<blockquote type="cite">
<pre wrap="">Thanks
On Mon, Sep 12, 2011 at 4:49 PM, Justin A. Lemkul <<a class="moz-txt-link-abbreviated" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>
<a class="moz-txt-link-rfc2396E" href="mailto:jalemkul@vt.edu"><mailto:jalemkul@vt.edu></a>> 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
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ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
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