[gmx-users] constraint error

[Justin Lemkul]

On 5/24/14, 4:46 AM, Lovika Moudgil wrote:
> Hi everyone...
>
> Can any body help me ...As i have an .itp file in which I have defined
> constraint and then I am defining this .itp file in my .top file....And
> with grompp command I got this error . I think I have defined constraints
> on right place. Than why this error ??Where I need to move constraints
> ??Please help me to understand this ...
>
> Fatal error:
> [ file gold_bulk.itp, line 16 ]:
> Atom index (2) in constraints out of bounds (1-1).
> This probably means that you have inserted topology section "constraints"
> in a part belonging to a different molecule than you intended to.
> In that case move the "constraints" section to the right molecule.
>

It seems that you have only 1 atom defined in the [moleculetype], but then you 
are defining a constraint involving atom 2, which does not exist.  The error is 
similar to a common mistake involving positions restraints:

http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds

If you need more specific advice, please provide us with the content of the 
problematic topology.

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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