<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span>In that directory I have created some other files by the gromacs command, but fail to on the top file. I will find the reason.</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 size="2" face="Arial"> <div style="margin: 5px 0px; padding: 0px; border: 1px solid rgb(204, 204, 204); height: 0px; line-height: 0; font-size: 0px;" class="hr" contentEditable="false" readonly="true"></div> <b><span style="font-weight: bold;">From:</span></b> Mark Abraham <Mark.Abraham@anu.edu.au><br> <b><span style="font-weight: bold;">To:</span></b> <br><b><span style="font-weight: bold;">Cc:</span></b> Discussion list for GROMACS users
<gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Friday, 9 March 2012 10:31 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] -p topol.top input/output error<br> </font> </div> <br><meta content="off" http-equiv="x-dns-prefetch-control"><div id="yiv225367066">
<div>
On 9/03/2012 11:24 PM, Dialing Pretty wrote:
<blockquote type="cite">
<div style="color: rgb(0, 0, 0); font-family: times new roman, new york, times, serif; font-size: 12pt; background-color: rgb(255, 255, 255);">
<div><span>Hi Mark, iy says</span></div>
<div><font size="1">"Program genbox, VERSION 4.0.5</font></div>
<div><font size="1">
</font></div>
<div><font size="1">Source code file: futil.c, line: 330</font></div>
<div><font size="1">
</font></div>
<div><font size="1">File input/output error:</font></div>
<div><font size="1">
</font></div>
<div><font size="1">fan1.top"</font></div>
<div><font size="1"> </font></div>
<div><font size="1">And there is no indication early steps
failure.</font></div>
<div><font size="1"> </font></div>
<div><font size="1">Any suggestions?</font></div>
</div>
</blockquote>
<br>
Either the tutorial is wrong (and you just happen to be the first to
notice), or you've done something wrong, such as working in a
directory where you cannot create files. There's lots of
possibilities, however.<br>
<br>
Mark<br>
<br>
<blockquote type="cite">
<div style="color: rgb(0, 0, 0); font-family: times new roman, new york, times, serif; font-size: 12pt; background-color: rgb(255, 255, 255);">
<div><font size="1"> </font></div>
<div><font size="1">Dialing</font></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 size="2" face="Arial"> <b><span style="font-weight: bold;">From:</span></b> Mark
Abraham <a class="yiv225367066moz-txt-link-rfc2396E" href="mailto:Mark.Abraham@anu.edu.au" rel="nofollow" target="_blank" ymailto="mailto:Mark.Abraham@anu.edu.au"><Mark.Abraham@anu.edu.au></a><br>
<b><span style="font-weight: bold;">To:</span></b>
Discussion list for GROMACS users
<a class="yiv225367066moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org" rel="nofollow" target="_blank" ymailto="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a> <br>
<b><span style="font-weight: bold;">Sent:</span></b>
Friday, 9 March 2012 10:18 PM<br>
<b><span style="font-weight: bold;">Subject:</span></b>
Re: [gmx-users] -p topol.top input/output error<br>
</font> </div>
<br>
<div id="yiv225367066">
<div> On 9/03/2012 10:52 PM, Dialing Pretty wrote:
<blockquote type="cite">
<div style="color: rgb(0, 0, 0); font-family: times new roman, new york, times, serif; font-size: 12pt; background-color: rgb(255, 255, 255);">
<div><span><font face="Arial"><font size="3">Dear
All,</font></font></span></div>
<div><span></span> </div>
<div><span><font face="Arial"><font size="3">When I
use gromacs 4.0.5 practice the on-line
tutorial on lysozyme, for</font></font></span></div>
<pre><font face="Arial"><font size="3">genbox -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top,</font></font></pre>
<pre><font face="Arial"><font size="3"> </font></font></pre>
<pre><font face="Arial"><font size="3">the output says <font size="1"><div>File input/output error:</div><div>topol.top</div></font></font></font></pre>
<pre><font face="Arial"><font size="3">Will you please give me some suggestions on how to solve the problem?</font></font></pre>
</div>
</blockquote>
<br>
This file should exist. It doesn't. Presumably some
previous step failed.<br>
<br>
Mark<br>
</div>
</div>
<br>
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</div>
</blockquote>
<br>
</div>
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