[gmx-users] MoleculeType not found

Gerrit Groenhof g.Groenhof at chem.rug.nl
Thu Sep 11 14:51:02 CEST 2003

Hi Raj,

Look in the ions.itp an pay attention to the #define directives.

 From what you wrote I think you are using a forcefield in which the
atomstype for Cl- is not simply Cl, but CL- or somethinf (Gromos96:
#ifdef _FF_GROMOS96 inions.itp). Thus in this case ad CL- 1 to your
topology file instead of Cl. Also do this in your .gro file, to avoid

Good luck,


> Just a quick question, hope someone can help.
> I've worked my way through the spider toxin tutorial by Dr Kerrigan, 
> and am starting MD on my own system.
> I've setup the water box and, added a Cl to balance out the +1 
> charge, run the energy minimisation and am at the position 
> restrained MD stage and when I initiate grompp i get the error 
> message:
> Fatal errol: moleculetype Cl not found
> I found one reference to this in the lists which said to remove the Cl 
> entry from ions.itp and save it as a separate file and link this to the 
> TOP file (include...).
> When I do this, I get another error message saying
> Fatal error: Protein contains no atoms.
> Any suggesitons?
> Hope someone can help
> Many thanks
> Raj Badhan
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