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Please leave the discussion on the mailing list, so that others can
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On 11/04/2012 10:53 PM, Lara Bunte wrote:
<blockquote
cite="mid:1334148819.63407.YahooMailNeo@web29404.mail.ird.yahoo.com"
type="cite">
<div style="color: rgb(0, 0, 0); background-color: rgb(255, 255,
255); font-family: times new roman,new york,times,serif;
font-size: 12pt;">
<div>Hi</div>
<div><br>
</div>
<div>How to do that? I searched the manual for "layer" and I
don't find something that helped. I also have no idea about
what distances.</div>
</div>
</blockquote>
<br>
There's no standard definition of a layer - it depends what you're
trying to do. A layer around a protein with a concavity might need
to be defined quite differently from a layer around a monatomic ion
or next to a hydrophobic phase boundary.<br>
<br>
Ultimately, you need to get some idea about distances :-) Look up
how long a water O-H bond is. Wikipedia will do. What does your
knowledge of the structure of water suggest about a likely range for
a O-H-O distance? How does that relate to how big a "layer" might
be? Do you care how rough the layer is? Do you care if your layer
has water molecule(s) between a water molecule and your solute? Use
g_select to select water atoms within some range of your solute and
look at the results.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:1334148819.63407.YahooMailNeo@web29404.mail.ird.yahoo.com"
type="cite">
<div style="color:#000; background-color:#fff; font-family:times
new roman, new york, times, serif;font-size:12pt">
<div> I have a small molecule in a big water box and I only want
one layer (later 2, 3, ..n) that I want to keep around the
molecule and remove the rest. <br>
</div>
<div><br>
</div>
<div>In appendix I put one of this .pdb files that you can see
what I mean. <br>
</div>
<div><br>
</div>
<div>Thanks for help</div>
<div><br>
</div>
<div>Greetings</div>
<div>Lara<br>
<span></span></div>
<div><br>
<span></span></div>
<div><span></span></div>
<div><br>
</div>
<div style="font-family: times new roman, new york, times,
serif; font-size: 12pt;">
<div style="font-family: times new roman, new york, times,
serif; font-size: 12pt;">
<div dir="ltr"> <font face="Arial" size="2">
<hr size="1"> <b><span style="font-weight:bold;">Von:</span></b>
Mark Abraham <a class="moz-txt-link-rfc2396E" href="mailto:mark.abraham@anu.edu.au"><mark.abraham@anu.edu.au></a><br>
<b><span style="font-weight: bold;">An:</span></b> Lara
Bunte <a class="moz-txt-link-rfc2396E" href="mailto:lara.bunte@yahoo.de"><lara.bunte@yahoo.de></a> <br>
<b><span style="font-weight: bold;">Gesendet:</span></b>
14:07 Mittwoch, 11.April 2012<br>
<b><span style="font-weight: bold;">Betreff:</span></b>
Re: [gmx-users] File editing - only one layer of water
around a molecule<br>
</font> </div>
<br>
<meta http-equiv="x-dns-prefetch-control" content="off">
<div id="yiv382240722">
<div> </div>
<div> </div>
<span>On 11/04/12, <b class="yiv382240722name">Lara Bunte
</b><a class="moz-txt-link-rfc2396E" href="mailto:lara.bunte@yahoo.de"><lara.bunte@yahoo.de></a> wrote:</span>
<blockquote style="BORDER-LEFT:#00f 1px
solid;PADDING-LEFT:13px;MARGIN-LEFT:0px;"
class="yiv382240722iwcQuote" type="cite">Hi<br>
<br>
I read g_select description and I still don't know how
to solve my problem. No if you have a pdb file with a
molecule in water. How to remove all the water except of
one layer? How could I do this with g_select? What other
solutions could be used, with i.e. other software?</blockquote>
<div> </div>
<div>First, define "a layer" in a way that suits what you
are trying to observe. Copy literature approaches if
suitable. Then seek to cast that definition in terms of
distances between atoms, which is all that you have to
work with.</div>
<div> </div>
<div>Mark </div>
<div> </div>
<blockquote style="BORDER-LEFT:#00f 1px
solid;PADDING-LEFT:13px;MARGIN-LEFT:0px;"
class="yiv382240722iwcQuote" type="cite">
<div class="yiv382240722mimepart yiv382240722text
yiv382240722plain"><br>
<br>
Greetings<br>
Lara<br>
<br>
<br>
<br>
<br>
<br>
<br>
----- Ursprüngliche Message -----<br>
Von: Mark Abraham <a class="moz-txt-link-rfc2396E" href="mailto:Mark.Abraham@anu.edu.au"><Mark.Abraham@anu.edu.au></a><br>
An: Discussion list for GROMACS users
<a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a><br>
CC: <br>
Gesendet: 14:27 Mittwoch, 4.April 2012<br>
Betreff: Re: [gmx-users] File editing - only one layer
of water around a molecule<br>
<br>
On 4/04/2012 7:27 PM, Lara Bunte wrote:<br>
> Hello<br>
> <br>
> I have a question about editing a pdb file.<br>
> <br>
> I have a molecule in a box of water as a pdb
file. I want to remove all water except of ONE layer
around he molecule. How to do that?<br>
> <br>
> <br>
> Do you know a software that is able to do that?
Do you know how it could work with programs like PyMol
or others?<br>
<br>
There's many ways to do it. The GROMACS way is to use
g_select with some geometric criterion for the layer
to generate an index group describing the layer, and
then using that with trjconv -n to take the subset out
of the trajectory file.<br>
<br>
Mark<br>
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