<html>
<head>
<style><!--
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
font-size: 10pt;
font-family:Tahoma
}
--></style></head>
<body class='hmmessage'><div dir='ltr'>
<div><div dir="ltr">Dear Sir/Madam,<div><br></div><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 href="http://www.cems.uvm.edu/~smanchu/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 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 ftp://ftp.gromacs
.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 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><span style="font-family:'Times New Roman';font-size:16px">> make clean</span></div><div><font face="'Times New Roman'" size="3">> </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 face="'Times New Roman'" color="#ff0000">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 face="'Times New Roman'" color="#ff0000">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;"><br></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 face="'Times New Roman'" color="#ff0000"><br></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><br></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><br></b></font></span></pre></div></div> </div></div> </div></body>
</html>