Christopher,<br><br>I am a novice in this field and have the same experience like you.<br>I hope this will help you: <br><br>1. Have you compared the molecule's name in topology file in [ molecules ] section and molecules's name in .itp file?
<br>2. Does residue names in the topology file match with the name in coordinate file? <br>If not, it is better to math them.<br><br>3. Or, rewrite .mpd file with Linux editor. <br>I don't know much about Linux. But when I rewrite .mpd file again it works.
<br><br>Seungpyo Hong<br><br><div><span class="gmail_quote">On 7/24/07, <b class="gmail_sendername">Moore, Jonathan (J)</b> <<a href="mailto:JMoore2@dow.com">JMoore2@dow.com</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div vlink="purple" link="blue" lang="EN-US">
<div dir="ltr" align="left"><span><font color="#0000ff" face="Arial" size="2">Christopher,</font></span></div>
<div dir="ltr" align="left"><span><font color="#0000ff" face="Arial" size="2"></font></span> </div>
<div dir="ltr" align="left"><span><font color="#0000ff" face="Arial" size="2">I'm afraid I don't have any other ideas. To confirm
if your editing method is OK, I would run a GROMACS example with an undmodified
.mdp file and then modify it (making some trivial change) by your method and see
if it still runs OK.</font></span></div>
<p><span lang="en-us"><font color="#0000ff" face="Brush Script MT" size="6">Jonathan</font></span> </p>
<p><span class="q"><span lang="en-us"><font color="#ff0000" face="Arial" size="2">____________________________</font></span> <br><span lang="en-us"><b><font color="#808080" face="Comic Sans MS" size="2">Jonathan Moore,
Ph.D.</font></b></span> <br><span lang="en-us"><font color="#808080" face="Arial" size="1">Research and Engineering Sciences - New Products</font></span> <br><span lang="en-us"><font color="#808080" face="Arial" size="1">
Core R&D</font></span>
<br><span lang="en-us"><font color="#808080" face="Arial" size="1">The Dow Chemical
Company</font></span> <br><span lang="en-us"><font color="#808080" face="Arial" size="1">1702 Building, Office 300E</font></span> <br><span lang="en-us"><font color="#808080" face="Arial" size="1">Midland, MI 48674 USA</font>
</span>
<br><span lang="en-us"><font color="#808080" face="Arial" size="1">Phone: (989)
636-9765 </font></span><br><span lang="en-us"><font color="#808080" face="Arial" size="1">Fax: (989) 636-4019</font></span> <br></span><span lang="en-us"><font color="#808080" face="Arial" size="1">E Mail: <a href="mailto:jmoore2@dow.com" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
jmoore2@dow.com</a></font></span> </p>
<div> </div><br>
<blockquote dir="ltr" style="margin-right: 0px;">
<div dir="ltr" align="left" lang="en-us">
<hr>
<font face="Tahoma" size="2"><b>From:</b> <a href="mailto:gmx-users-bounces@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">gmx-users-bounces@gromacs.org</a>
[mailto:<a href="mailto:gmx-users-bounces@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">gmx-users-bounces@gromacs.org</a>] <b>On Behalf Of </b>Christopher
Stiles<br><b>Sent:</b> Monday, July 23, 2007 4:42 PM<span class="q"><br><b>To:</b>
<a href="mailto:gmx-users@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">gmx-users@gromacs.org</a><br></span><b>Subject:</b> Re: Re: [gmx-users] number of
coordinates in coordinate file does not match topology<br></font><br></div>
<div></div>
<div><span class="q"><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">Jonathan,</span></font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;"> I had originally done that but I read through the archives and found out that that was an issue. To solve this issue I used the following command in Vim: "set ff=unix" and then I wrote it. So I do not believe that it is an issue any longer as I mentioned on the walk through of my steps at
<a href="http://cs86.com/CNSE/SWNT.htm" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">http://cs86.com/CNSE/SWNT.htm</a>. </span></font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">
</span></font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">Do you have any other ideas on why this might be happening? If so please let me know, and thank you for your help so far!</span></font>
</pre><pre><font face="Cou
rier New" size="2"><span style="font-size: 10pt;"> </span></font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">Also please let me know if that command in vim would solve the problem.</span>
</font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;"> </span></font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">~Christopher Stiles </span></font></pre><pre><font face="Courier New" size="2">
<span style="font-size: 10pt;">College</span></font> of Nanoscale Science and Engineering (CNSE)</pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">State University of New York, Albany, New York 12203, USA
</span></font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;"> </span></font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">> </span></font></pre><pre><font face="Courier New" size="2">
<span style="font-size: 10pt;">>Christopher,</span></font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">> </span></font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">
>When I've had this problem before (# of coordinates in coordinate file does not match topology (0)), it has been because >I edited the mdp file under Windows (mismatch between Windows and unix end-of-line characters). Is it possible that you >have done the same? If so, try to run your mdp thr
<br> ough the dos2unix utility.</span></font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">> </span></font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">>
</span></font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">>Jonathan </span></font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">> </span></font></pre><pre>
<font face="Courier New" size="2"><span style="font-size: 10pt;">>____________________________ </span></font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">>Jonathan Moore, Ph.D. </span>
</font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">>Research and Engineering Sciences - New Products </span></font></pre></span><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">
>Core R&D <<br> /SPAN></span></font></pre><span class="q"><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">>The Dow Chemical Company </span></font></pre><pre><font face="Courier New" size="2">
<span style="font-size: 10pt;">>1702 Building, Office 300E </span></font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">>Midland, MI 48674 USA </span></font></pre><pre><font face="Courier New" size="2">
<span style="font-size: 10pt;">>Phone: (989) 636-9765 </span></font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">>Fax: (989) 636-4019 </span></font></pre><pre><font face="Courier New" size="2">
<span style="font-size: 10pt;">>E Mail: <a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">jm<br> oore2 at dow.com</a> </span></font></pre>
<pre><font face="Courier New" size="2"><span style="font-size: 10pt;">> </span></font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">> </span></font></pre><pre><font face="Courier New" size="2">
<span style="font-size: 10pt;">> </span></font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">> </span></font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">
> _____ </span></font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">> </span></font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">>>From: <a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
gmx-users-bounces at gromacs.org</a> [mailto:<a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">gmx-users-bounces at gromacs.org</a>] On Behalf Of Christopher Stiles
</span></font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">>>Sent: Monday, July 23, 2007 12:08 PM</span></font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">
>>To: <a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">gmx-users at gromacs.org</a></span></font></pre><pre><font face="Courier New" size="2">
<span style="font-size: 10pt;">>>Subject: Re: [gmx-users] number of coordinates in coordinate file does not match topology</span></font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">>>
</span></font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">>> </span></font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">>> </span></font></pre><pre>
<font face="Courier New" size="2"><span>>>I have already asked about this but I think maybe I did not give enough information so I made the following page:</span></font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">
>> </span></font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">>><a href="http://cs86.com/CNSE/SWNT.htm" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">http://cs86.com/CNSE/SWNT.htm
</a></span></font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">>>It outlines every step I have taken and where I am stuck is at the end with grompp when it spits out the following >>error:
</span></font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">>> </span></font></pre></span><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">>>********************************************************************************************************<
<br> /o:p></span></font></pre><span class="q"><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">>> </span></font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">>>Fatal error:
</span></font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">>> </span></font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">>>number of coordinates in coordinate file (SWNT_6_6_144_b4em.gro, 699)
</span></font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">>> </span></font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">>> does not match topology (SWNT_6_6_144.top, 0)
</span></font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">>> </span></font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">>> also it updates the SWNT_6_6_144.top file to: SWNT_6_6_144.top
</span></font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">>>********************************************************************************************************</span></font></pre>
<pre><font face="Courier New" size="2"><span style="font-size: 10pt;">>>I have looked through both the *.gro and *.top files and I can not find anything wrong with them; maybe one of you will >>have better luck.
</span></font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">>> </span></font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">>>Any help or advice is greatly appreciated!
</span></font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">>> </span></font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">>> </span></font></pre><pre>
<font face="Courier New" size="2"><span style="font-size: 10pt;">>> </span></font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">>>~Christopher Stiles </span></font></pre><pre><font face="Courier New" size="2">
<span style="font-size: 10pt;">>>College of Nanoscale Science and Engineering (CNSE)</span></font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">>>State University of New York, Albany, New York 12203, USA
</span></font></pre>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">>> </span></font></p></span></div></blockquote></div>
<br>_______________________________________________<br>gmx-users mailing list <a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a onclick="return top.js.OpenExtLink(window,event,this)" href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">
http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a onclick="return top.js.OpenExtLink(window,event,this)" href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search
</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to <a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users-request@gromacs.org">
gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a onclick="return top.js.OpenExtLink(window,event,this)" href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php
</a><br></blockquote></div><br>