[gmx-users] position_restraints

Justin A. Lemkul jalemkul at vt.edu
Tue Oct 19 13:19:02 CEST 2010

#ZHAO LINA# wrote:
> Hi,
>  Fatal error:
> [ file protein.itp, line 9 ]:
> Atom index (5) in position_restraints out of bounds (1-1).
> This probably means that you have inserted topology section 
> "position_restraints"
> in a part belonging to a different molecule than you intended to.
> In that case move the "position_restraints" section to the right molecule.

As the error message indicates, your #include statement is in the wrong place. 
In the topology, order matters.  The [position_restraints] directive must be 
#included after the relevant [moleculetype] directive, and not after anything else.


> Thanks for any clue. The part belongs to the one I want to restraints. I 
> mean, the molecule is right.
> Thanks,
> lina


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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