[gmx-users] MoleculeType not found

[Gerrit Groenhof]

Hi Raj.

Did you by any chance include your cl_ion.itp at the top of your
topolgy file, i.e. before the definition of the protein and the
#include "ffG43a2.itp"
 directive??

if you make your own chloride.itp file it should look like this (or
something like this :-):

[ moleculetype ]
Cl              1

[ atoms ]
; id    at type res nr  residu name     at name  cg nr  charge
1       Cl      1       Cl              Cl       1      -1


Where the atomtype should match the atomtype in the itp and atp files
of the forcefield you're using.

and then you should include it somehwere afer the protein topology
entries. After the #include spc.itp for instance. That should work.

Good luck again,


Gerrit





> 
> 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
> > > 
> > > _______________________________________________
> > > gmx-users mailing list
> > > gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please don't post (un)subscribe requests to the list. Use the 
> > > www interface or send it to gmx-users-request at gromacs.org.
> > > 
> > 
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the 
> > www interface or send it to gmx-users-request at gromacs.org.
> 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
>