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<DIV dir=ltr align=left><SPAN class=706402519-23072007><FONT face=Arial
color=#0000ff size=2>Christopher,</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=706402519-23072007><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=706402519-23072007><FONT face=Arial
color=#0000ff size=2>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.</FONT></SPAN></DIV>
<DIV> </DIV><!-- Converted from text/rtf format -->
<P><SPAN lang=en-us><FONT face="Brush Script MT" color=#0000ff
size=6>Jonathan</FONT></SPAN> </P>
<P><SPAN lang=en-us><FONT face=Arial color=#ff0000
size=2>____________________________</FONT></SPAN> <BR><SPAN lang=en-us><B><FONT
face="Comic Sans MS" color=#808080 size=2>Jonathan Moore,
Ph.D.</FONT></B></SPAN> <BR><SPAN lang=en-us><FONT face=Arial color=#808080
size=1>Research and Engineering Sciences - New Products</FONT></SPAN> <BR><SPAN
lang=en-us><FONT face=Arial color=#808080 size=1>Core R&D</FONT></SPAN>
<BR><SPAN lang=en-us><FONT face=Arial color=#808080 size=1>The Dow Chemical
Company</FONT></SPAN> <BR><SPAN lang=en-us><FONT face=Arial color=#808080
size=1>1702 Building, Office 300E</FONT></SPAN> <BR><SPAN lang=en-us><FONT
face=Arial color=#808080 size=1>Midland, MI 48674 USA</FONT></SPAN>
<BR><SPAN lang=en-us><FONT face=Arial color=#808080 size=1>Phone: (989)
636-9765 </FONT></SPAN><BR><SPAN lang=en-us><FONT face=Arial color=#808080
size=1>Fax: (989) 636-4019</FONT></SPAN> <BR><SPAN lang=en-us><FONT face=Arial
color=#808080 size=1>E Mail: jmoore2@dow.com</FONT></SPAN> </P>
<DIV> </DIV><BR>
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<DIV class=OutlookMessageHeader lang=en-us dir=ltr align=left>
<HR tabIndex=-1>
<FONT face=Tahoma size=2><B>From:</B> gmx-users-bounces@gromacs.org
[mailto:gmx-users-bounces@gromacs.org] <B>On Behalf Of </B>Christopher
Stiles<BR><B>Sent:</B> Monday, July 23, 2007 12:08 PM<BR><B>To:</B>
gmx-users@gromacs.org<BR><B>Subject:</B> Re: [gmx-users] number of coordinates
in coordinate file does not match topology<BR></FONT><BR></DIV>
<DIV></DIV>
<DIV class=Section1>
<P class=MsoNormal><FONT face=Arial size=2><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">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></P>
<P class=MsoNormal><FONT face=Arial size=2><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Arial"><A
href="http://cs86.com/CNSE/SWNT.htm">http://cs86.com/CNSE/SWNT.htm</A><o:p></o:p></SPAN></FONT></P>
<P class=MsoNormal><FONT face=Arial size=2><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">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></P>
<P class=MsoNormal><FONT face=Arial size=2><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">********************************************************************************************************<o:p></o:p></SPAN></FONT></P>
<P class=MsoNormal><FONT face="Times New Roman" size=3><SPAN
style="FONT-SIZE: 12pt">Fatal error:<U1:P></U1:P></SPAN></FONT><FONT
face=Arial size=2><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Arial"><o:p></o:p></SPAN></FONT></P>
<P class=MsoNormal
style="mso-margin-top-alt: auto; mso-margin-bottom-alt: auto"><FONT
face="Times New Roman" size=3><SPAN style="FONT-SIZE: 12pt">number of
coordinates in coordinate file (SWNT_6_6_144_b4em.gro,
699)<U1:P></U1:P></SPAN><o:p></o:p></FONT></P>
<P class=MsoNormal
style="mso-margin-top-alt: auto; mso-margin-bottom-alt: auto"><FONT
face="Times New Roman" size=3><SPAN
style="FONT-SIZE: 12pt">
does not match topology (SWNT_6_6_144.top,
0)<U1:P></U1:P></SPAN><o:p></o:p></FONT></P>
<P class=MsoNormal
style="mso-margin-top-alt: auto; mso-margin-bottom-alt: auto"><FONT
face="Times New Roman" size=3><SPAN
style="FONT-SIZE: 12pt"><U1:P> </U1:P>also it updates the
SWNT_6_6_144.top file to: <A
href="http://cs86.com/CNSE/files/SWNT_6_6_144_post_grommp.top"><FONT
color=black><SPAN
style="COLOR: windowtext">SWNT_6_6_144.top</SPAN></FONT></A><BR></SPAN></FONT><FONT
face=Arial size=2><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">********************************************************************************************************</SPAN></FONT><BR><FONT
face=Arial size=2><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">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><o:p></o:p></P>
<P class=MsoNormal><FONT face=Arial size=2><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">Any help or advice is greatly
appreciated!<o:p></o:p></SPAN></FONT></P>
<P class=MsoNormal><FONT face=Arial size=2><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Arial"><o:p> </o:p></SPAN></FONT></P><PRE><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">~Christopher Stiles <o:p></o:p></SPAN></FONT></PRE><PRE><st1:place w:st="on"><st1:PlaceType w:st="on"><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">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 face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">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>
<P class=MsoNormal><FONT face=Arial size=2><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Arial"><o:p> </o:p></SPAN></FONT></P></DIV></BLOCKQUOTE></BODY></HTML>