<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;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><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 <Mark.Abraham@anu.edu.au><br> <b><span style="font-weight: bold;">An:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org> <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><meta http-equiv="x-dns-prefetch-control" content="off"><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>
<blockquote type="cite">
<div 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;">
<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 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 rel="nofollow" class="yiv104663948moz-txt-link-rfc2396E" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a> <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 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 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 rel="nofollow" class="yiv104663948moz-txt-link-rfc2396E" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a>
<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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