[gmx-users] Distance restraints
spoel at xray.bmc.uu.se
Tue Oct 4 18:44:33 CEST 2005
On Tue, 2005-10-04 at 11:44 -0400, Bob Johnson wrote:
> 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
right now you cannot have bonded interactions between different
molecules. You'll have to merge the topologies into one. A script to do
this might dwell on the gromacs site.
> 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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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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