[gmx-users] Including a position restraint file

[David]

On Fri, 2005-08-12 at 17:36 -0400, Bob Johnson wrote:
> 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
> #ifdef POSRES_NANOTUBE
> #include "posre_nanotube.itp"
> #endif
This has to go straight after the cnt_26 as it is part of the topology
of the nanotube. Grompp thinks it is part of the water top now.

> 
> [ system ]
> ;Name
> Biosensor
> 
> [ 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?
> Thanks,
> Bob Johnson
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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