[gmx-users] Grompp error

[Mark Abraham]

Farid Sa'adedin wrote:
> Dear Users,
> 
> I have added Cl ion to my peptide in water system pdb and topology files.
> But I have a problem when I run grompp:
> 
> Fatal Error: Atoms in the .top are not numbered consecutively from 1.
> 
> The pdb is numbered correctly and I have added the the spc.itp and 
> clion.itp to the topology file.

I would have a look at the .top file and see how the atoms are not 
numbered consecutively from 1, and do something appropriate about it.

Perhaps you should use genbox to add chloride and water before using 
pdb2gmx to generate your .top file.

Mark