[gmx-users] fatal error during running grompp

Mark Abraham Mark.Abraham at anu.edu.au
Tue Dec 9 23:27:27 CET 2008

arie wibowo wrote:
> Dear all, 
> I am a beginner using gromacs. when I start to run gromacs, the calculation always stop in grompp due to fatal error was appeared. the information below the fatal error is "number of coordinates in coordinate file (minimized_water.gro, 26791) does not match topology file (aki.top, 1555)". but when I try to look aki.top file, there are already 1 molecules of protein, 78 molecules of SOL and 8412 molecules of SOL in the end of this file, so I think topology file must contain more than 1555 atom. I have already change .mdp file manually using gedit because I see in internet this error can also occur because .mdp file has been edited under Windows, but the problem still occur. is there any help or suggestion?

You've probably got something wrong with your .top file format, but we 
can't guess what. Have a read of the relevant bits of chapter 5, 
including the examples there.


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