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<div class=Section1><pre><font size=2 face="Courier New"><span
style='font-size:10.0pt'>Jonathan,<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'> 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">http://cs86.com/CNSE/SWNT.htm</a>. <o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>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!<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>Also please let me know if that command in vim would solve the problem.<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>~Christopher Stiles <o:p></o:p></span></font></pre><pre><st1:place
w:st="on"><st1:PlaceType w:st="on"><font size=2 face="Courier New"><span
style='font-size:10.0pt'>College</span></font></st1:PlaceType> of <st1:PlaceName
w:st="on">Nanoscale</st1:PlaceName></st1:place> Science and Engineering (CNSE)<o:p></o:p></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>State <st1:PlaceType
w:st="on">University</st1:PlaceType> of <st1:PlaceName w:st="on">New York</st1:PlaceName>, <st1:place
w:st="on"><st1:City w:st="on">Albany</st1:City>, <st1:State w:st="on">New York</st1:State> <st1:PostalCode
w:st="on">12203</st1:PostalCode>, <st1:country-region w:st="on">USA</st1:country-region></st1:place><o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>Christopher,<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>> <o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>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 through the dos2unix utility.<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>> <o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>Jonathan <o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>____________________________ <o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>Jonathan Moore, Ph.D. <o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>Research and Engineering Sciences - New Products <o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>Core R&D <o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>The Dow Chemical Company <o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>1702 Building, Office 300E <o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>><st1:place w:st="on"><st1:City
w:st="on">Midland</st1:City>, <st1:State w:st="on">MI</st1:State> <st1:PostalCode
w:st="on">48674</st1:PostalCode> <st1:country-region w:st="on">USA</st1:country-region></st1:place> <o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>Phone: (989) 636-9765 <o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>Fax: (989) 636-4019 <o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>E Mail: <a
href="http://www.gromacs.org/mailman/listinfo/gmx-users">jmoore2 at dow.com</a> <o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>> <o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>> _____ <o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>>From: <a
href="http://www.gromacs.org/mailman/listinfo/gmx-users">gmx-users-bounces at gromacs.org</a> [mailto:<a
href="http://www.gromacs.org/mailman/listinfo/gmx-users">gmx-users-bounces at gromacs.org</a>] On Behalf Of Christopher Stiles<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>>Sent: Monday, July 23, 2007 12:08 PM<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>>To: <a
href="http://www.gromacs.org/mailman/listinfo/gmx-users">gmx-users at gromacs.org</a><o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>>Subject: Re: [gmx-users] number of coordinates in coordinate file does not match topology<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>>I have already asked about this but I think maybe I did not give enough information so I made the following page:<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>><a
href="http://cs86.com/CNSE/SWNT.htm">http://cs86.com/CNSE/SWNT.htm</a><o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>>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:<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>>********************************************************************************************************<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>>Fatal error:<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>>number of coordinates in coordinate file (SWNT_6_6_144_b4em.gro, 699)<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>> does not match topology (SWNT_6_6_144.top, 0)<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>> also it updates the SWNT_6_6_144.top file to: SWNT_6_6_144.top<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>>********************************************************************************************************<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>>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.<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>>Any help or advice is greatly appreciated!<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>> <o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>>~Christopher Stiles <o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>><st1:place
w:st="on"><st1:PlaceType w:st="on">College</st1:PlaceType> of <st1:PlaceName
w:st="on">Nanoscale</st1:PlaceName></st1:place> Science and Engineering (CNSE)<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>><st1:PlaceType
w:st="on">State</st1:PlaceType> <st1:PlaceType w:st="on">University</st1:PlaceType> of <st1:State
w:st="on">New York</st1:State>, <st1:place w:st="on"><st1:City w:st="on">Albany</st1:City>, <st1:State
w:st="on">New York</st1:State> <st1:PostalCode w:st="on">12203</st1:PostalCode>, <st1:country-region
w:st="on">USA</st1:country-region></st1:place><o:p></o:p></span></font></pre>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>>><o:p> </o:p></span></font></p>
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