[gmx-users] MoleculeType not found

[Raj Badhan]

In reply to Gerrit response,
Thanks for e-mail.
I tried doing this eairler and it seems to fixes the CL issue, but this 
is where the:

Fatal error: Moleculetype Protein contains no atoms


comes in.
Hope you or anyone could help.
Thanks for the quick response!
Raj Badhan
> 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
> warnings..
> 
> Good luck,
> 
> Gerrit
> 
> > 
> > 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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