[gmx-users] Distance restraints

Bob Johnson robertjo at physics.upenn.edu
Tue Oct 4 17:44:04 CEST 2005

Hello everyone,
My system consists of an infinite carbon nanotube, a single stranded DNA
molecule and water. I would like to constrain the distance between certain
atoms of the DNA and the nanotube. However, I have three different topology
files: one for the nanotube, one for the DNA, and one for the water. I would
like to use the following distance restraint:

806  2167 6  0.3  30000

The 6 is for the simple harmonic potential for the atomic separation. 806 is the
atom number for a carbon nanotube atom and the 2167 is the atom number for a
nitrogen on the DNA. Since I have three separate topology files I'm not sure
where to put this statement. My main topology file is shown below.

;Topology file

;Biosensor force field parameters
#include "ffbiosensor.itp"

;Topology include files
#include "13_0_12L.itp"
#include "ssdna_seq1.itp"
#include "water.itp"

[ system ]

[ molecules ]
; name          number
13_0_12L        1
ssdna_seq1      1
water           13639

When putting the [ bonds ] statement here grompp generates the message:
Fatal error: [ file "biosensor.top", line 24 ]:
             Atom index (806) in bonds out of bounds (1-3)

Where should I define this bond at?
Bob Johnson
PhD candidate
Dept. of Physics & Astronomy
University of Pennsylvania

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