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On 13/04/2012 8:17 PM, Lara Bunte wrote:
<blockquote
cite="mid:1334312240.50097.YahooMailNeo@web29406.mail.ird.yahoo.com"
type="cite">
<div style="color: rgb(0, 0, 0); background-color: rgb(255, 255,
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font-size: 12pt;">
<div>Thanks for that but where in this do I give Gromacs my pdb.
file. From where do g_select use this information? <br>
</div>
<div><br>
</div>
<div>What I have is a pdb file. <br>
</div>
</div>
</blockquote>
<br>
Look at g_select -h for -f and -s. Like every GROMACS tool, .pdb is
one of the file types you can use instead of a trajectory or run
input file in cases where (as here) that makes sense.<br>
<br>
On a more general note, I hope you've done all the GROMACS tutorial
material you can find - this question is one example of the kind of
usage "general knowledge" that can often be acquired that way.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:1334312240.50097.YahooMailNeo@web29406.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><br>
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<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>
Discussion list for GROMACS users
<a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a> <br>
<b><span style="font-weight: bold;">Gesendet:</span></b>
12:06 Freitag, 13.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>
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<div id="yiv104663948">
<div> On 13/04/2012 8:01 PM, Lara Bunte wrote:
<blockquote 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 Mark</div>
<div><br>
</div>
<div>Could you please give me for that the prompt
how to write this in the console. <br>
</div>
<div><br>
</div>
<div>"All atoms of a residue LIG within 0.5 nm of a
protein (with a custom name):<br>
"Close to protein" resname LIG and within 0.5 of
group "Protein" "<br>
</div>
<div><br>
</div>
<div>So how to put this into the console? I often
found in the manual text that I don't know how to
concretely type in into the bash console? <br>
</div>
<div><br>
</div>
<div>Thanks for helping me and sorry for my
questions. I am a noob :-( <br>
</div>
</div>
</blockquote>
<br>
The text for g_select -h in the upcoming GROMACS release
will make this clearer, as others have struggled with
this part recently.<br>
<br>
g_select -other -options -select '"Close to protein"
resname LIG and within 0.5 of group "Protein"'<br>
<br>
works for that example. Note carefully the use of single
and double quotes.<br>
<br>
Mark<br>
<br>
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style="color:#000;background-color:#fff;font-family:times
new roman, new york, times, serif;font-size:12pt;">
<div><span></span></div>
<div><br>
</div>
<div>Greetings</div>
<div>Lara</div>
<div><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;">
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<hr size="1"> <b><span
style="font-weight:bold;">Von:</span></b>
Mark Abraham <a moz-do-not-send="true"
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<b><span style="font-weight:bold;">An:</span></b>
Discussion list for GROMACS users <a
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<br>
<b><span style="font-weight:bold;">Gesendet:</span></b>
11:51 Freitag, 13.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>
<div id="yiv104663948">
<div> On 13/04/2012 7:29 PM, Lara Bunte wrote:
<blockquote 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>I read g_select -select 'help all'
and I understand nothing of that. <br>
</div>
<div><br>
</div>
<div>In general one have a molecule
(valences closed by hydrogen) and a
water box around it. How to select
only the protein with the first water
layers, say one layer? </div>
<div><br>
</div>
<div>Please give me an example how to do
this with gromacs. I read the examples
in g_select -select 'help all' and I
have no Idea what they are talking
about. <br>
</div>
</div>
</blockquote>
<br>
Surely you can see that the example<br>
<br>
All atoms of a residue LIG within 0.5 nm of
a protein (with a custom name):<br>
"Close to protein" resname LIG and within
0.5 of group "Protein" <br>
<br>
is very similar to what would be needed for
all water residues within some distance of
your solute.<br>
<br>
VMD uses a similar approach. BioPython
probably likewise. There's no genie going to
wave the magic create-a-layer wand. You need
to learn how to create a layer from a
definition that suits you, because you'll
probably have to vary that definition until
you're happy with the outcome.<br>
<br>
Mark<br>
<br>
<blockquote type="cite">
<div
style="color:#000;background-color:#fff;font-family:times
new roman, new york, times,
serif;font-size:12pt;">
<div><br>
</div>
<div>Thanks for help</div>
<div>Greetings</div>
<div>Lara</div>
<div><br>
</div>
<div><br>
</div>
<span></span>
<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
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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
moz-do-not-send="true"
rel="nofollow"
class="yiv104663948moz-txt-link-rfc2396E"
ymailto="mailto:Mark.Abraham@anu.edu.au" target="_blank"
href="mailto:Mark.Abraham@anu.edu.au"><Mark.Abraham@anu.edu.au></a><br>
<b><span
style="font-weight:bold;">An:</span></b>
Discussion list for GROMACS
users <a moz-do-not-send="true"
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<br>
<b><span
style="font-weight:bold;">Gesendet:</span></b>
19:26 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>
On 12/04/2012 3:24 AM, Justin A.
Lemkul wrote:<br>
> <br>
> <br>
> Lara Bunte wrote:<br>
>> Could you please give how
g_select is used?<br>
<br>
Reading g_select -h might have led
you to try g_select -select 'help'<br>
<br>
>> Is there a tutorial for
that?<br>
>> <br>
> <br>
> g_select -select 'help all'<br>
> <br>
> The information contained
therein is very extensive, so be
sure to read it thoroughly. It will
fill several terminal windows
explaining the syntax and providing
examples.<br>
<br>
... and search Google for some
examples.<br>
<br>
Mark<br>
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