[gmx-users] grompp error

[Anton Feenstra]

Steffen Haerterich wrote:

> 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
[...]

Right - as I said, molecule names *within* your topology must be
consistent, as you nicely demonstrate: 'Protein' and 'Protein' works,
'Protei' and 'Protei' also works but the other combinations don't.

> 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

Right - the 'Protein' in your energygrps corresponds to a default index
group that is always constructed, but its name is not related to the
name of the [moleculetype]. All residues whose name are in $GMXLIB/aminoacids.dat
are considered 'Protein'.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|