[gmx-users] fatal error message

Derrick Guang Yuh Lee k24dgyl at mun.ca
Fri Jun 3 02:58:42 CEST 2005

Dear Ahmed,

Your error,

Fatal error: number of coordinates in coordinate file (conf.gro, 648)
	     does not match topology (topol.top, 0)

means that you need to adjust your topology file, for some reason or
another, it appears that the molecules in your system were not defined,
i.e. the number of proteins in your system or the number of water
molecules. this is an example of part of the topology file in one of my

[ molecules ]
; name  number
DPPC    128
SOL     3655

i think, chances are that the molecule types are not listed, hence
why your topol.top has 0 atoms. I hope this helps.


 - Derrick Lee

 Derrick Guang Yuh Lee
 Department of Mathematics and Statistics / Department of Biochemistry
 Memorial University of Newfoundland
 k24dgyl at mun.ca / derrickglee at hotmail.com

"a teacher is never a giver of truth - he is a guide, a pointer to the
truth that each student must find for himself. a good teacher is merely a
                                                              - bruce lee

On Thu, 2 Jun 2005, Lakhani, Ahmed Ashiqali wrote:

> Hi Lee,
> Thank you for responeding.
> I did run grompp, however I am getting this fatal error messages (look at
> the bottom of this message)  I think it has to do with cpp
> "creating statusfile for 1 node...
> checking input for internal consistency...
> calling C:\Documents and Settings\Ahmed
> Lakhani\Desktop\gromacs\share\tutor\meth
> anol\cpp...
> 'C:\Documents' is not recognized as an internal or external command,
> operable program or batch file.
> cpp exit code: 1
> Tried to execute: 'C:\Documents and Settings\Ahmed
> Lakhani\Desktop\gromacs\share
> \tutor\methanol\cpp  -IC:\Documents and Settings\Ahmed
> Lakhani\Desktop\gromacs\s
> hare\top  topol.top > gromppa00600'
> The 'C:\Documents and Settings\Ahmed
> Lakhani\Desktop\gromacs\share\tutor\methano
> l\cpp' command is defined in the .mdp file
> processing topology...
> processing coordinates...
> Fatal error: number of coordinates in coordinate file (conf.gro, 648)
>              does not match topology (topol.top, 0)"
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