[gmx-users] Grompp failed under double precision

[Justin A. Lemkul]

Jack Shultz wrote:
> We have a workflow going, and I switched to double precision because
> of the LINCS issues. I got this error now with grompp. I don't think
> anything else is different other than double precision, but I included
> the logs for this.
> 
> -------------------------------------------------------
> Program grompp_d, VERSION 4.0.5
> Source code file: toppush.c, line: 1273
> 
> Fatal error:
> [ file spce.itp, line 32 ]:
> Atom index (1) in bonds out of bounds (1-0).
> This probably means that you have inserted topology section "bonds"
> in a part belonging to a different molecule than you intended to.
> In that case move the "bonds" section to the right molecule.
> -------------------------------------------------------
> 

Please see the following:

http://www.gromacs.org/Documentation/Errors#Atom_index_(1)_in_bonds_out_of_bounds

Particularly of interest is the section within about the AMBER force fields, for 
which the default spc.itp is incompatible.

-Justin


-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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