<br>Hi Mark,<br><br>The -dist option says- print all the atoms in group 2 that are
closer than a certain distance to the center of mass of group 1.<br>That means it should give me the distance from OW to protein atom.<br><br>And when am already specifying only one atom from protein ie say 1322. why do i get this kind of output-<br>
<br>t: 275 20230 SOL 62618 OW 0.341434 (nm)<br>t: 275 22019 SOL 67985 OW 0.171584 (nm)<br>t: 276 10768 SOL 34232 OW 0.303328 (nm)<br>t: 276 20230 SOL 62618 OW 0.325176 (nm)<br>t: 276 22019 SOL 67985 OW 0.187259 (nm)<br>
t: 277 10768 SOL 34232 OW 0.306008 (nm)<br>t: 277 20230 SOL 62618 OW 0.326195 (nm)<br>t: 277 22019 SOL 67985 OW 0.181089 (nm)<br>t: 278 10768 SOL 34232 OW 0.274507 (nm)<br>t: 278 22019 SOL 67985 OW 0.292652 (nm)<br>
t: 279 10618 SOL 33782 OW 0.319922 (nm)<br>t: 280 10618 SOL 33782 OW 0.330082 (nm)<br>t: 280 22019 SOL 67985 OW 0.330203 (nm)<br>t: 281 8273 SOL 26747 OW 0.278731 (nm)<br>t: 281 10618 SOL 33782 OW 0.325434 (nm)<br>
t: 281 11535 SOL 36533 OW 0.200327 (nm)<br>t: 281 17036 SOL 53036 OW 0.343946 (nm)<br>t: 282 8273 SOL 26747 OW 0.256558 (nm)<br>t: 282 11535 SOL 36533 OW 0.327147 (nm)<br>t: 283 8273 SOL 26747 OW 0.165061 (nm)<br>
t: 283 10618 SOL 33782 OW 0.306578 (nm)<br>t: 283 17191 SOL 53501 OW 0.333075 (nm)<br>t: 284 8273 SOL 26747 OW 0.19427 (nm)<br>t: 284 10618 SOL 33782 OW 0.321927 (nm)<br>t: 284 17191 SOL 53501 OW 0.30832 (nm)<br>
<br><br><br><br><div class="gmail_quote">On Tue, Sep 13, 2011 at 10:40 AM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div bgcolor="#FFFFFF" text="#000000"><div class="im">
On 13/09/2011 2:27 PM, <a href="mailto:aiswarya.pawar@gmail.com" target="_blank">aiswarya.pawar@gmail.com</a> wrote:
<blockquote type="cite">
<pre>Iam -dist option because I need the distance between two groups</pre>
</blockquote>
<br></div>
That is not what g_dist -dist does. Please read g_dist -h.<div class="im"><br>
<br>
<blockquote type="cite">
<pre> excluding -dist gives me X,Y,Z output which I don't want.</pre>
</blockquote>
<br></div>
And other output which you do, but you have to use -o to get it.
Read g_dist -h.<div class="im"><br>
<br>
<blockquote type="cite">
<pre> And am not specifying an -o.</pre>
</blockquote>
<br></div>
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><font color="#888888">
<br>
Mark</font><div><div></div><div class="h5"><br>
<br>
<blockquote type="cite">
<pre>Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!
-----Original Message-----
From: "Justin A. Lemkul" <a href="mailto:jalemkul@vt.edu" target="_blank"><jalemkul@vt.edu></a>
Date: Mon, 12 Sep 2011 22:35:28
To: <a href="mailto:aiswarya.pawar@gmail.com" target="_blank"><aiswarya.pawar@gmail.com></a>; Discussion list for GROMACS users<a href="mailto:gmx-users@gromacs.org" target="_blank"><gmx-users@gromacs.org></a>
Reply-To: <a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>
Subject: Re: [gmx-users] g_dist error
<a href="mailto:aiswarya.pawar@gmail.com" target="_blank">aiswarya.pawar@gmail.com</a> wrote:
</pre>
<blockquote type="cite">
<pre>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>
</blockquote>
<pre>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>Thanks
Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!
-----Original Message-----
From: "Justin A. Lemkul" <a href="mailto:jalemkul@vt.edu" target="_blank"><jalemkul@vt.edu></a>
Sender: <a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a>
Date: Mon, 12 Sep 2011 07:52:54
To: Discussion list for GROMACS users<a href="mailto:gmx-users@gromacs.org" target="_blank"><gmx-users@gromacs.org></a>
Reply-To: <a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>,
Discussion list for GROMACS users <a href="mailto:gmx-users@gromacs.org" target="_blank"><gmx-users@gromacs.org></a>
Subject: Re: [gmx-users] g_dist error
aiswarya pawar wrote:
</pre>
<blockquote type="cite">
<pre>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>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>Thanks
On Mon, Sep 12, 2011 at 4:49 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>
<a href="mailto:jalemkul@vt.edu" target="_blank"><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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Department of Biochemistry
Virginia Tech
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</pre>
</blockquote>
<pre></pre>
</blockquote>
<pre></pre>
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