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On 9/03/2012 10:58 PM, a a wrote:
<blockquote cite="mid:COL118-W36B69648D6ACA19637302DA3540@phx.gbl"
type="cite">
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<div dir="ltr">Dear Sir/Madam,
<div><br>
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<div>I am trying to install the GROMACS to my new
workstation. As my old one is not belong to me, I cannot
install VMD to it. Please kindly help to instruct if I
did anything wrong here. Many thanks.</div>
<div>
<div><br>
</div>
<div>Follow the steps in <a moz-do-not-send="true"
href="http://www.cems.uvm.edu/%7Esmanchu/gromacs_installation.html"
style="font-size:10pt" target="_blank">http://www.cems.uvm.edu/~smanchu/gromacs_installation.html</a><span
style="font-size:10pt">, </span><span
style="font-size:10pt">I have done the installation
fftw-3.0.1 at my "/Catherine/Gromacs/fftw-3.0.1"
directory.</span></div>
<div><br>
</div>
<div>Follow the steps in <a moz-do-not-send="true"
href="http://fertoledo.wordpress.com/2012/01/17/how-to-calculate-cosine-content-in-amber/"
style="font-size:10pt" target="_blank">http://fertoledo.wordpress.com/2012/01/17/how-to-calculate-cosine-content-in-amber/</a>,
i.e. [<span style="font-size:10pt">wget
<a class="moz-txt-link-freetext" href="ftp://ftp.gromacs">ftp://ftp.gromacs</a>
.org/pub/gromacs/gromacs-4.5.4.tar.gz], I have
downloaded the gromacs to my Catherine/Gromacs/
folder.</span></div>
<div><br>
</div>
<div><span style="font-size:10pt">Follow the steps in </span><a
moz-do-not-send="true"
href="http://www.gromacs.org/Downloads/Installation_Instructions"
style="font-size:10pt" target="_blank">http://www.gromacs.org/Downloads/Installation_Instructions</a><span
style="font-size:10pt">, I have start installing the
GROMACS.</span><span style="font-size:10pt"> </span></div>
<div><span style="font-size:10pt"><br>
</span></div>
<div><span style="font-family:'Times New
Roman';font-size:12pt">> tar -xzvf
gromacs-4.5.4.tar.gz</span>
</div>
<div><span style="font-family:'Times New
Roman';font-size:12pt">> cd </span><span
style="font-family:'Times New Roman';font-size:16px">gromacs-4-5-4</span></div>
</div>
</div>
</div>
</div>
</blockquote>
<br>
The instruction for this command is wrong, because this is not the
directory created by the previous command. Please inform the author
of the tutorial.<br>
<br>
Mark<br>
<br>
<blockquote cite="mid:COL118-W36B69648D6ACA19637302DA3540@phx.gbl"
type="cite">
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<div>
<div><span style="font-family:'Times New
Roman';font-size:16px">> make clean</span></div>
<div><font size="3" face="'Times New Roman'">> </font><span
style="background-color:rgb(255, 255,
255);font-family:inherit;line-height:1.5;font-size:10pt;border-top-width:0px;border-right-width:0px;border-bottom-width:0px;border-left-width:0px;border-style:initial;border-color:initial;font-style:inherit;margin-right:0px;margin-bottom:0px;margin-left:0px;outline-width:0px;outline-style:initial;outline-color:initial;padding-top:0px;padding-right:0px;padding-bottom:0px;padding-left:0px;vertical-align:baseline">./configure
--prefix=/usr/local/gromacs --program-suffix=""</span></div>
<div><span style="background-color:rgb(255, 255,
255);font-family:inherit;line-height:1.5;font-size:10pt;border-top-width:0px;bord
er-right-width:0px;border-bottom-width:0px;border-left-width:0px;border-style:initial;border-color:initial;font-style:inherit;margin-right:0px;margin-bottom:0px;margin-left:0px;outline-width:0px;outline-style:initial;outline-color:initial;padding-top:0px;padding-right:0px;padding-bottom:0px;padding-left:0px;vertical-align:baseline">>
make</span></div>
<div><span style="line-height:19px">> make install</span></div>
<div><font color="#707070"><span style="line-height:19px"><b><br>
</b></span></font></div>
<div><font face="'Times New Roman'"><span
style="line-height:19px">However, when I do make
clean, following error message appear.</span></font></div>
<div>
<pre style="border-top-width:0px;border-right-width:0px;border-bottom-width:0px;border-left-width:0px;border-style:initial;border-color:initial;margin-bottom:1.154em;outline-width:0px;outline-style:initial;outline-color:initial;padding-top:1.538em;padding-right:1.538em;padding-bottom:1.538em;padding-left:1.538em;vertical-a
lign:baseline;background-image:initial;background-attachment:initial;background-origin:initial;background-clip:initial;background-color:rgb(255, 255, 255)"><span style="border-top-width:0px;border-right-width:0px;border-bottom-width:0px;border-left-width:0px;border-style:initial;border-color:initial;margin-right:0px;margin-bottom:0px;margin-left:0px;outline-width:0px;outline-style:initial;outline-color:initial;padding-top:0px;padding-right:0px;padding-bottom:0px;padding-left:0px;vertical-align:baseline;line-height:19px"><font color="#ff0000" face="'Times New Roman'">make: *** No rule to make target `clean'. Stop.</font></span></pre>
<pre style="border-top-width:0px;border-right-width:0px;border-bottom-width:0px;border-left-width:0px;border-style:initial;border-color:initial;margin-bottom:1.154em;outline-width:0px;outline-style:initial;outline-color:initial;padding-top:1.538em;padding-right:1.538em;padding-bottom:1.538em;padding-left:1.538em;vertical-align:baseline;background
-image:initial;background-attachment:initial;background-origin:initial;background-clip:initial;background-color:rgb(255, 255, 255)"><span style="border-top-width:0px;border-right-width:0px;border-bottom-width:0px;border-left-width:0px;border-style:initial;border-color:initial;margin-right:0px;margin-bottom:0px;margin-left:0px;outline-width:0px;outline-style:initial;outline-color:initial;padding-top:0px;padding-right:0px;padding-bottom:0px;padding-left:0px;vertical-align:baseline;line-height:19px"><font face="'Times New Roman'">When I continously doing the make after ./configure step, I found the following error message:</font></span></pre>
<pre style="border-top-width:0px;border-right-width:0px;border-bottom-width:0px;border-left-width:0px;border-style:initial;border-color:initial;margin-bottom:1.154em;outline-width:0px;outline-style:initial;outline-color:initial;padding-top:1.538em;padding-right:1.538em;padding-bottom:1.538em;padding-left:1.538em;vertical-align:baseline;back
ground-image:initial;background-attachment:initial;background-origin:initial;background-clip:initial;background-color:rgb(255, 255, 255)"><span style="border-top-width:0px;border-right-width:0px;border-bottom-width:0px;border-left-width:0px;border-style:initial;border-color:initial;margin-right:0px;margin-bottom:0px;margin-left:0px;outline-width:0px;outline-style:initial;outline-color:initial;padding-top:0px;padding-right:0px;padding-bottom:0px;padding-left:0px;vertical-align:baseline;line-height:19px"><font color="#ff0000" face="'Times New Roman'">make: *** No targets specified and no makefile found. Stop.</font></span></pre>
<pre style="border-top-width:0px;border-right-width:0px;border-bottom-width:0px;border-left-width:0px;border-style:initial;border-color:initial;margin-bottom:1.154em;outline-width:0px;outline-style:initial;outline-color:initial;padding-top:1.538em;padding-right:1.538em;padding-bottom:1.538em;padding-left:1.538em;vertical-align:baseline;background-image
:initial;background-attachment:initial;background-origin:initial;background-clip:initial;background-color:rgb(255, 255, 255)"><font face="'Times New Roman'"><span style="line-height:19px">Could you please kindly instruct if I have done any things stupidly wrong? Following is the log file for the configure.log, please kindly help.</span></font></pre>
<pre style="border-top-width:0px;border-right-width:0px;border-bottom-width:0px;border-left-width:0px;border-style:initial;border-color:initial;margin-bottom:1.154em;outline-width:0px;outline-style:initial;outline-color:initial;padding-top:1.538em;padding-right:1.538em;padding-bottom:1.538em;padding-left:1.538em;vertical-align:baseline;background-image:initial;background-attachment:initial;background-origin:initial;background-clip:initial;background-color:rgb(255, 255, 255)"><font face="'Times New Roman'"><span style="line-height:19px">Catherine</span></font></pre>
<pre style="border-top-width:0px;border-right-width:0px;border-bot
tom-width:0px;border-left-width:0px;border-style:initial;border-color:initial;margin-bottom:1.154em;outline-width:0px;outline-style:initial;outline-color:initial;padding-top:1.538em;padding-right:1.538em;padding-bottom:1.538em;padding-left:1.538em;vertical-align:baseline;background-image:initial;background-attachment:initial;background-origin:initial;background-clip:initial;background-color:rgb(255, 255, 255)"><font face="'Times New Roman'"><span style="line-height: 19px;">
</span></font></pre>
<div><font face="'Times New Roman'"><span
style="line-height:19px"><br>
</span></font></div>
<div><font face="'Times New Roman'">
<div><br>
</div>
</font></div>
<pre style="border-top-width:0px;border-right-width:0px;border-bottom-width:0px;border-left-width:0px;border-style:initial;border-color:initial;margin-bottom:1.154em;outline-width:0px;outline-style:initial;outline-color:initial;padding-top:1.538em;padding-right:1.538em;padding-bottom:1.538em;padding-left:1.538em;vertical-align:bas
eline;background-image:initial;background-attachment:initial;background-origin:initial;background-clip:initial;background-color:rgb(255, 255, 255)"><span style="border-top-width:0px;border-right-width:0px;border-bottom-width:0px;border-left-width:0px;border-style:initial;border-color:initial;margin-right:0px;margin-bottom:0px;margin-left:0px;outline-width:0px;outline-style:initial;outline-color:initial;padding-top:0px;padding-right:0px;padding-bottom:0px;padding-left:0px;vertical-align:baseline;line-height:19px"><font color="#ff0000" face="'Times New Roman'">
</font></span></pre>
<pre style="border-top-width:0px;border-right-width:0px;border-bottom-width:0px;border-left-width:0px;border-style:initial;border-color:initial;margin-bottom:1.154em;outline-width:0px;outline-style:initial;outline-color:initial;padding-top:1.538em;padding-right:1.538em;padding-bottom:1.538em;padding-left:1.538em;vertical-align:baseline;background-image:initial;background-attachment:initial;backgro
und-origin:initial;background-clip:initial;background-color:rgb(255, 255, 255)"><span style="border-top-width:0px;border-right-width:0px;border-bottom-width:0px;border-left-width:0px;border-style:initial;border-color:initial;margin-right:0px;margin-bottom:0px;margin-left:0px;outline-width:0px;outline-style:initial;outline-color:initial;padding-top:0px;padding-right:0px;padding-bottom:0px;padding-left:0px;vertical-align:baseline;line-height:19px"><font color="#707070" face="Monaco, 'Courier New', Courier, monospace"><b>
</b></font></span></pre>
<pre style="border-top-width:0px;border-right-width:0px;border-bottom-width:0px;border-left-width:0px;border-style:initial;border-color:initial;margin-bottom:1.154em;outline-width:0px;outline-style:initial;outline-color:initial;padding-top:1.538em;padding-right:1.538em;padding-bottom:1.538em;padding-left:1.538em;vertical-align:baseline;background-image:initial;background-attachment:initial;background-origin:initial;background-clip:in
itial;background-color:rgb(255, 255, 255)"><span style="border-top-width:0px;border-right-width:0px;border-bottom-width:0px;border-left-width:0px;border-style:initial;border-color:initial;margin-right:0px;margin-bottom:0px;margin-left:0px;outline-width:0px;outline-style:initial;outline-color:initial;padding-top:0px;padding-right:0px;padding-bottom:0px;padding-left:0px;vertical-align:baseline;line-height:19px"><font color="#707070" face="Monaco, 'Courier New', Courier, monospace"><b>
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