[gmx-users] Group protein not found in index file

[Justin A. Lemkul]

Lara Bunte wrote:
> Hello 
> 
> 
> I want to use the command 
> 
> grompp -n index.ndx -f pr.mdp -p topol.top -c em.gro -o pr.tpr
> 
> and I got the error:
> 
> Fatal error:
> Group protein not found in index file.
> Group names must match either [moleculetype] names
> or custom index group names,in which case you
> must supply an index file to the '-n' option of grompp.
> 
> 
> The index.ndx was created by make_ndx and looks like: 
> 
> 
> [ System ]
>    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15
>   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30
>   31   32
> [ Isoalloxazin ]
>    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15
>   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30
>   31   32
> [ ISO ]
>    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15
>   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30
>   31   32
> 
> 
> In residuetypes.dat I declared ISO as Isoalloxazine
> 

This is not a valid specifier.  You can only use Protein, DNA, RNA, Ion, or 
Other as groups.  You could conceivably then define ISO as Protein in order to 
circumvent the error.

> What ist the problem?
> 

In your .mdp file, grompp is finding a group called "protein."  You do not have 
such a group.  The group names are in the directives denoted within [], so in 
your case, the only valid names for groups to be specified are System, 
Isoalloxazin, and ISO.  If you specify anything else, you have to create a group 
and name it such that grompp finds a match between the .mdp file and the .ndx file.

-Justin

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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