[gmx-users] grompp error

[Steffen Haerterich]

Hallo Anton,
thanks for your comment. 
After some testing I consider it to be absolutely correct but there is some truth 
my own statement, too: 

1. Adjusting "Protein" to "Protei" within the system:
 [ molecules ]
  ; Compound          #mols
  Protei                     1
 
-> Described error with grompp

2. Adjusting "Protein" to "Protei" within the topology:

  [ moleculetype ]
  ; name                nrexcl
  Protei                  3

-> Described error with grompp

3. Adjusting both to "Protei":

  [ moleculetype ]
  ; name                nrexcl
  Protei                  3

  [ molecules ]
  ; Compound          #mols
  Protei                     1

-> Now it works!

I have to add that I did not mention any index-groups within my mdp-file. So 
this is only testing the topology-files. 
Going further with an mdp using groups:

Applying energygrps = Protein
-> still works

Applying enerygrps = Protei
-> Error reoccurs

So it seems that the error reported by Dinesh might be (perhaps and under 
some certain circumstances) due to an error within the topology and/or mdp-
file.
I hope that I did not miss something important. 

Regards,
  Steffen

On 5 Aug 2004 at 9:21, Anton Feenstra wrote:

> Steffen Haerterich wrote:
> 
> > Hallo!
> > Check if your Protein is named Protein in your topology of the 
> [...]
> > Sometimes a chainidentifier may creep into the name. (e.g. Protein_X)
> > You would then have to adjust the name within the topologie and/or 
> > mdp-file. I don't know if Gromacs is case-sensitive.
> > I hope this is of any help .
> 
> This is not relevant. Molecule names are used within the topology, to
> define the molecule and build the system consisting of molecules.
> 
> The group options grompp complains about, refer to the Index Groups,
> as defined by default, or by your .ndx file.
> 
> While this may seem confusing, the reason is simple. By having the groups
> (and group names) independent of molecule definitions (and names), one can
> define groups consisting of many molecules, or even of part of one molecule.
> 
> 
> -- 
> Groetjes,
> 
> Anton
>   _____________ _______________________________________________________
> |             |                                                       |
> |  _   _  ___,| K. Anton Feenstra                                     |
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Steffen Härterich
Emil Fischer Centrum
FAU Erlangen-Nürnberg
Schuhstr. 19, 91052 Erlangen
Tel.: 09131/85-24111