[gmx-users] grompp

Justin A. Lemkul jalemkul at vt.edu
Tue Nov 3 12:53:11 CET 2009

leila karami wrote:
> Hi
> I used grompp command but follow fatal error appeared:
> Atom index (1) in settles out of bounds (1-0).
> This probably means that you have inserted topology section "settles" in 
> a part belonging to a different molecule than you intended to.
> In that case move the "settles" section to the right molecule.
> please guide me


Beyond that, search the list archive; this comes up quite often when you've 
improperly formatted the topology.


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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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