Atom index out of bound

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1

GROMACS version: 2019.6
GROMACS modification: Yes/No
Here post your question :I am encountering this error while running equilibrium simulations for my system on Ubuntu 18.04
Command line:
gmx grompp -f npt.mdp -r nvt.gro -c nvt.gro -t nvt.cpt -p top.top -o npt.tpr

Setting the LD random seed to 709664446
Generated 2926 of the 2926 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2926 of the 2926 1-4 parameter combinations

ERROR 1 [file CA_restr.itp, line 5]:
Atom index (5) in position_restraints out of bounds (1-3).
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.

Can someone help me to fix this.
Thank you so much for your help. I really appreciate it!
The description of the file CA_restr.itp is in the txt file
CA_restr.txt (30.7 KB)

2

I guess that the error message is right. Attaching only your restraint file doesn’t help. I guess you included that file somewhere too late and thus made the restraints apply to the water molecule type instead of a protein. Include the restraint file in the molecule section of the correct molecule.

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3

Thanks for the helpful advice! I have found the problem.