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

[Christopher Stiles]

Jonathan,
        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
http://cs86.com/CNSE/SWNT.htm. 
 
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!
 
Also please let me know if that command in vim would solve the problem.
 
~Christopher Stiles 
College of Nanoscale Science and Engineering (CNSE)
State University of New York, Albany, New York 12203, USA
 
> 
>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
<http://www.gromacs.org/mailman/listinfo/gmx-users>  
> 
> 
> 
> 
>  _____  
> 
>>From: gmx-users-bounces at gromacs.org
<http://www.gromacs.org/mailman/listinfo/gmx-users>
[mailto:gmx-users-bounces at gromacs.org
<http://www.gromacs.org/mailman/listinfo/gmx-users> ] On Behalf Of
Christopher Stiles
>>Sent: Monday, July 23, 2007 12:08 PM
>>To: gmx-users at gromacs.org
<http://www.gromacs.org/mailman/listinfo/gmx-users> 
>>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
>>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: 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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