[gmx-users] number of coordinates in coordinate file does not match topology

[Moore, Jonathan (J)]

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: jmoore2 at dow.com 

 


  _____  

From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Christopher Stiles
Sent: Monday, July 23, 2007 12:08 PM
To: gmx-users at gromacs.org
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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