[gmx-users] problem with position restraints

[K.A. Feenstra]

Ben Tehan wrote:
> 
> Hello fellow gromacs users,
>         I am having some unexpected problems whilst trying to do initial
> dynamics with position restraints. Has anyone seen this problem before?
> I have included the first few lines of both my posre.itp and
> post_min.gro files  to have a look at.
> 
> >grompp -f pr.mdp -c post_min.gro -p 1a1v.top -o pr.tpr
> 
> Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
> checking input for internal consistency...
> calling /lib/cpp...
> processing topology...
> Generated 135 of the 1081 non-bonded parameter combinations
> Cleaning up temporary file gromppdOxKKF
> Fatal error: [ file "posre.itp", line 9 ]:
>              Atom index (4) in position_restraints out of bounds (1-1)
[...snip...]

You probably have inserted the posre.itp after e.g. ions.itp in your
.top file. The issue here is that position restraints are molecule-
based, so they must appear inside the proper [ molecule_type ]
section in the .top file. 'ions.itp', for example, contains a 
[ molecule_type ] section for each of the separate ions, the same
will be true for lipids.itp or an .itp file for a ligand or co-factor.


-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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