[gmx-users] Position restraints for a part of the protein

X.Periole X.Periole at rug.nl
Wed Jul 26 17:02:17 CEST 2006

> I used 'genpr' to generate the 'posre.itp' file as I did 
>many other times
> to restrain the entire protein leaving the solvent free.
> Once I run 'grompp' I get the following message:
> "Fatal error: [ file "1_Cter.top", line 7895 ]:
> Atom index (152) in position_restraints out of bounds 
> where atom 152 is the first atom in the protein that I 
>want to restraint.

It looks like the molecule you try to apply the position
restrain to is a solvent molecules (3 atoms). You should
check that grompp takes the right posres.itp for the


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