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On 15/04/2012 1:15 AM, Lara Bunte wrote:
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cite="mid:1334416502.23282.YahooMailNeo@web29404.mail.ird.yahoo.com"
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<div>Hi Justin</div>
<div><br>
</div>
<div>The difference in my <br>
<span></span></div>
<div><br>
</div>
<div> g_select -s molecule_in_water.pdb -select '"Close to ISO"
resname SOL and within 0.5 of group "ISO"'</div>
<div><br>
</div>
<div>and your</div>
<div><br>
</div>
<div>g_select -s molecule_in_water.pdb -select '"Close to ISO"
resname SOL and within 0.5 of resname ISO'</div>
<div><br>
</div>
<div>is, that the last ISO is not in quotation marks. Could you
please explain? <br>
</div>
</div>
</blockquote>
<br>
The significant difference is that you refer to "group "ISO""
without defining that group (since it is not defined by default,
unlike the example group named Protein), and Justin refers to the
RESidue NAMEd "ISO" with "resname ISO".<br>
<br>
As you would know if you had more experience with the Unix command
line, quotation marks are sometimes necessary to help delineate what
groups of words make sense where (e.g. in English<br>
Mark said "Justin said do this"<br>
differs from<br>
"Mark said," Justin said, "do this"). Sometimes you can get away
with no quotation marks around something if the purpose of the
quotation marks is merely grouping and the thing is only one word
long. So the selection string needs quotation marks around "Close to
ISO" to group those words to create a new index group with that
name, the command line needs quotation marks around the selection
string to group all those words, but Justin's resname might/can
survive without. Unlike a reader of the written word, the UNIX shell
parser is not endowed with higher intellect, so one needs to use
different quotation marks to handle nesting, or explicitly delineate
the nesting... but that is a topic you can Google about at your
leisure.<br>
<br>
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<div><br>
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<div>With your command I got this time no error but I got other
stuff that I don't understand: <br>
</div>
<div><br>
</div>
<div>1.)</div>
<div> I got this warnings:</div>
<div><br>
</div>
<div>WARNING: masses and atomic (Van der Waals) radii will be
determined<br>
based on residue and atom names. These numbers can
deviate<br>
from the correct mass and radius of the atom type.<br>
</div>
</div>
</blockquote>
<br>
Unlike programs that just guess stuff and don't ever tell you about
it (which explains 99% of the posts on this list about the behaviour
of VMD), GROMACS warns you that it's going to have to make guesses
about your input since it comes in .pdb form. Input in .tpr form
would allow the tool to make definitive assignments. If you had an
atom named "HG" that was intended to be mercury or a hydrogen on a
gamma carbon, you should go check the results made sense. So you
should judge for yourself how weird your atom names are with respect
to standard PDB naming, and whether you even use the masses or VDW
radii in your calculation.<br>
<br>
<blockquote
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<div><br>
<br>
WARNING: if there are broken molecules in the trajectory file,<br>
they can not be made whole without a run input file<br>
</div>
<div><br>
</div>
<div>Can I ignore this or is this serious? <br>
</div>
</div>
</blockquote>
<br>
I've now improved this error message in the code. Molecules can be
"broken" across periodic boundaries under some circumstances. Since
you're using .pdb input, and GROMACS tools make no attempt to use
the PDB format for atomic connectivity even if it is present,
GROMACS is warning you that you need to consider this aspect
yourself. Inspecting the relevant coordinates in the file or a
visualization program and comparing them with the location of the
periodic box might be necessary, depending how your input file was
created. You will normally know things about your files that GROMACS
cannot know.<br>
<br>
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type="cite">
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<div><br>
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<div>2.)</div>
<div>My output is one file called size.xvg. It contains</div>
<div><br>
</div>
<div># This file was created Sat Apr 14 16:55:56 2012<br>
# by the following command:<br>
# g_select -s molecule_in_water.pdb -select "Close to ISO"
resname SOL and within 0.5 of resname ISO<br>
#<br>
# g_select is part of G R O M A C S:<br>
#<br>
# Green Red Orange Magenta Azure Cyan Skyblue<br>
#<br>
@ title "Selection size"<br>
@ xaxis label "Time (ps)"<br>
@ yaxis label "Number"<br>
@TYPE xy<br>
# Selections:<br>
# "Close to ISO" resname SOL and within 0.5 of resname ISO<br>
#<br>
@ view 0.15, 0.15, 0.75, 0.85<br>
@ legend on<br>
@ legend box on<br>
@ legend loctype view<br>
@ legend 0.78, 0.8<br>
@ legend length 2<br>
@ s0 legend "Close to ISO"<br>
0.000 848.000<br>
<br>
</div>
<div>What is the interpretation of this? What I need is a new
pdb. file that has to contain only the molecule ISO and the
water layer SOL around it. Is this possible with g_select?</div>
</div>
</blockquote>
<br>
No. g_select has defaulted silently to the behaviour for g_select
-os, which you can read about in g_select -h. That's no good to you,
of course. You need an index group that you can use with another
tool (e.g. trjconv) to actually make the selection. (Future GROMACS
versions will be able to do this in one step, but that nirvana yet
awaits.) For the exercise, please look up the correct output option
for this from g_select -h.<br>
<br>
Mark<br>
<br>
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<div><br>
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<div>Thanks for helping me. <br>
</div>
<div>Greetings</div>
<div>Lara<br>
</div>
<div><br>
</div>
<div><br>
</div>
<div>p.s.</div>
<div>I use yahoo. I tried to find an "answer to all" option or
something like that. Again after pressing answer the mail
should go only to Justin. I put the mailing list in cc. Is
here someone using yahoo also and know how to fix this?<br>
</div>
<div><br>
</div>
<div><br>
<span></span></div>
<div><br>
<span></span></div>
<div><span></span></div>
<div><br>
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<hr size="1"> <b><span style="font-weight:bold;">Von:</span></b>
Justin A. Lemkul <a class="moz-txt-link-rfc2396E" href="mailto:jalemkul@vt.edu"><jalemkul@vt.edu></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>; 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>
16:56 Samstag, 14.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>
<br>
<br>
Lara Bunte wrote:<br>
> I still got the problem. What is wrong in this command:<br>
> <br>
> g_select -s molecule_in_water.pdb -select '"Close to
ISO" resname SOL and within 0.5 of group "ISO"'<br>
> <br>
> In the pdb. file ISO is for the molecule and SOL for
the water.<br>
> <br>
> Please help<br>
> <br>
<br>
The above command assumes "ISO" is a default group, like
"Protein" or something else. You can make selections based
on any arbitrary residue name with something like the
following:<br>
<br>
g_select -s molecule_in_water.pdb -select '"Close to ISO"
resname SOL and within 0.5 of resname ISO'<br>
<br>
Does that work?<br>
<br>
-Justin<br>
<br>
-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]vt.edu | (540) 231-9080<br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<br>
<br>
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