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