[gmx-users] Including a position restraint file

Bob Johnson robertjo at physics.upenn.edu
Fri Aug 12 23:36:55 CEST 2005

Hello everyone,
I am trying to include a restraint file in my simulation. Here's a copy of my
topology file

; Biosensor

;Include force field files
#include "ffbiosensor.itp"

;Include molecule topologies
#include "cnt_26_0.itp"            ;nanotube topology
#include "ssdna_nopairs.itp"       ;ssdna topology
#include "water.itp"               ;water topology

;Position restraints on nanotube
#include "posre_nanotube.itp"

[ system ]

[ molecules ]
;Molecule name          Number of molecules
cnt_26_0                1
ssdna                   1
water                   124

Grompp gives errors when I have the include statement in the position as shown.
It says:
Fatal error: [ file "posre_nanotube.itp", line 8 ]:
Atom index (4) in position_restraints out of bounds (1-3)

I have 2080 atoms in my nanotube. Where do I put the include statement?
Bob Johnson

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