[gmx-users] MoleculeType not found

[Raj Badhan]

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