Christopher, 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.
Jonathan ____________________________ Jonathan Moore, Ph.D. Research and Engineering Sciences - New Products Core R&D The Dow Chemical Company 1702 Building, Office 300E Midland, MI 48674 USA Phone: (989) 636-9765 Fax: (989) 636-4019 E Mail: [EMAIL PROTECTED] _____ From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Christopher Stiles Sent: Monday, July 23, 2007 12:08 PM To: [email protected] Subject: Re: [gmx-users] number of coordinates in coordinate file does not match topology I have already asked about this but I think maybe I did not give enough information so I made the following page: http://cs86.com/CNSE/SWNT.htm <http://cs86.com/CNSE/SWNT.htm> 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: ******************************************************************************************************** Fatal error: number of coordinates in coordinate file (SWNT_6_6_144_b4em.gro, 699) does not match topology (SWNT_6_6_144.top, 0) also it updates the SWNT_6_6_144.top file to: <http://cs86.com/CNSE/files/SWNT_6_6_144_post_grommp.top> SWNT_6_6_144.top ******************************************************************************************************** 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. Any help or advice is greatly appreciated! ~Christopher Stiles College of Nanoscale Science and Engineering (CNSE) State University of New York, Albany, New York 12203, USA
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