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<DIV dir=ltr align=left><SPAN class=792553721-23072007><FONT face=Arial
color=#0000ff size=2>Christopher,</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=792553721-23072007><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=792553721-23072007><FONT face=Arial
color=#0000ff 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><!-- 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>
<BLOCKQUOTE dir=ltr style="MARGIN-RIGHT: 0px">
<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 4:42 PM<BR><B>To:</B>
gmx-users@gromacs.org<BR><B>Subject:</B> Re: Re: [gmx-users] number of
coordinates in coordinate file does not match topology<BR></FONT><BR></DIV>
<DIV></DIV>
<DIV class=Section1><PRE><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">Jonathan,<o:p></o:p></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">http://cs86.com/CNSE/SWNT.htm</A>. <o:p></o:p></SPAN></FONT></PRE><PRE><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt"><o:p> </o:p></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!<o:p></o:p></SPAN></FONT></PRE><PRE><FONT face="Cou
rier New" size=2><SPAN style="FONT-SIZE: 10pt"><o:p> </o:p></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.<o:p></o:p></SPAN></FONT></PRE><PRE><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt"><o:p> </o:p></SPAN></FONT></PRE><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><PRE><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt"><o:p> </o:p></SPAN></FONT></PRE><PRE><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">><o:p> </o:p></SPAN></FONT></PRE><PRE><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">>Christopher,<o:p></o:p></SPAN></FONT></PRE><PRE><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">> <o:p></o:p></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
ough the dos2unix utility.<o:p></o:p></SPAN></FONT></PRE><PRE><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">> <o:p></o:p></SPAN></FONT></PRE><PRE><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">><o:p> </o:p></SPAN></FONT></PRE><PRE><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">>Jonathan <o:p></o:p></SPAN></FONT></PRE><PRE><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">><o:p> </o:p></SPAN></FONT></PRE><PRE><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">>____________________________ <o:p></o:p></SPAN></FONT></PRE><PRE><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">>Jonathan Moore, Ph.D. <o:p></o:p></SPAN></FONT></PRE><PRE><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">>Research and Engineering Sciences - New Products <o:p></o:p></SPAN></FONT></PRE><PRE><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">>Core R&D <o:p></o:p><
/SPAN></FONT></PRE><PRE><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">>The Dow Chemical Company <o:p></o:p></SPAN></FONT></PRE><PRE><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">>1702 Building, Office 300E <o:p></o:p></SPAN></FONT></PRE><PRE><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">><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 face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">>Phone: (989) 636-9765 <o:p></o:p></SPAN></FONT></PRE><PRE><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">>Fax: (989) 636-4019 <o:p></o:p></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">jm
oore2 at dow.com</A> <o:p></o:p></SPAN></FONT></PRE><PRE><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">><o:p> </o:p></SPAN></FONT></PRE><PRE><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">> <o:p></o:p></SPAN></FONT></PRE><PRE><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">><o:p> </o:p></SPAN></FONT></PRE><PRE><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">><o:p> </o:p></SPAN></FONT></PRE><PRE><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">> _____ <o:p></o:p></SPAN></FONT></PRE><PRE><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">><o:p> </o:p></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">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 face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">>>Sent: Monday, July 23, 2007 12:08 PM<o:p></o:p></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">gmx-users at gromacs.org</A><o:p></o:p></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<o:p></o:p></SPAN></FONT></PRE><PRE><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">>><o:p> </o:p></SPAN></FONT></PRE><PRE><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">>><o:p> </o:p></SPAN></FONT></PRE><PRE><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">>><o:p> </o:p></SPAN></FONT></PRE><PRE><FONT face="Courier New" size=2><SPAN style="FON
T-SIZE: 10pt">>>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 face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">>><o:p> </o:p></SPAN></FONT></PRE><PRE><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">>><A href="http://cs86.com/CNSE/SWNT.htm">http://cs86.com/CNSE/SWNT.htm</A><o:p></o:p></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:<o:p></o:p></SPAN></FONT></PRE><PRE><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">>><o:p> </o:p></SPAN></FONT></PRE><PRE><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">>>********************************************************************************************************<o:p><
/o:p></SPAN></FONT></PRE><PRE><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">>><o:p> </o:p></SPAN></FONT></PRE><PRE><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">>>Fatal error:<o:p></o:p></SPAN></FONT></PRE><PRE><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">>><o:p> </o:p></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)<o:p></o:p></SPAN></FONT></PRE><PRE><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">>><o:p> </o:p></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)<o:p></o:p></SPAN></FONT></PRE><PRE><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">>><o:p> </o:p></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<o:p></o:p></SPAN></FONT></PRE><PRE><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">>>********************************************************************************************************<o:p></o:p></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.<o:p></o:p></SPAN></FONT></PRE><PRE><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">>><o:p> </o:p></SPAN></FONT></PRE><PRE><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">>>Any help or advice is greatly appreciated!<o:p></o:p></SPAN></FONT></PRE><PRE><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">>><o:p> </o:p></SPAN
></FONT></PRE><PRE><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">>> <o:p></o:p></SPAN></FONT></PRE><PRE><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">>><o:p> </o:p></SPAN></FONT></PRE><PRE><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">>>~Christopher Stiles <o:p></o:p></SPAN></FONT></PRE><PRE><FONT face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">>><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 face="Courier New" size=2><SPAN style="FONT-SIZE: 10pt">>><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 face=Arial size=2><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">>><o:p> </o:p></SPAN></FONT></P></DIV></BLOCKQUOTE></BODY></HTML>