[gmx-users] Problems using grompp and amber force field

Mark Abraham Mark.Abraham at anu.edu.au
Tue May 8 02:53:37 CEST 2007

root wrote:
> Dear GROMACS user:
> Erik and Tom thanks by the comments, too. Sorry, I read the FAQ pages of
> http://folding.stanford.edu and now I understand your comments.  
> We tried with cpp = /lib/cpp -traditional in the mdp file. The warning
> desapears, but the error messages is similar.
> (Fatal error:
>>>> Atoms in the .top are not numbered consecutively from 1
>>>> -------------------------------------------------------
>>>> We tested the dick.top file, and we verified that the atoms
>>>         are numbered
>>>> consecutively from 1 to 758.)

Have you inspected the #included files as well? The way cpp works, any 
file #included is literally dropped into its parent file, so if you had 
something wrong in such an #inclusion you'd need to fix that.


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