[gmx-users] Position restraint file

Kai Zhuang kai.zhuang at gmail.com
Thu Aug 11 22:30:19 CEST 2005

i did this when i was working on a similar system:

create 2 pdb filies (1 DNA, 1 nanotube), call it A.pdb, B.pdb
do pdb2gmx twice, get 2 gro files, 2 top files, 2 posre.itp files.
cat the 2 gro files together, edit the file, fix the atom number
manually. call it C.gro
create a new top file that connects the four topology files together,
call it C.top

#include "A.top"
#include "B.top"

#ifdef POSRES
#include "A_posre.itp"
#include "B_posre.itp"

look at A.top and B.top, any overlapping declarations, put them in C.top.
basically, you want to strip A.top and B.top to just the information
about the atoms.
leave the A_posre.top and B_posre.top be.

should work.

On 8/11/05, Bob Johnson <robertjo at physics.upenn.edu> wrote:
> Hello,
> I am studying the interactions between single stranded DNA and a carbon
> nanotube. I am using the Amber force field for the DNA molecule. When the two
> systems (dna and nanotube) are brought together, the nanotube is severely
> deformed by the presence of the dna. I wanted to try restraining the positions
> of the nanotube since it is probable that the nanotube structure remains the
> same upon insertion of a dna molecule. How would I format the posre.itp file?
> Do I specify the coordinates of all the nanotube carbon atoms along with a
> force constant? I'm unsure of the syntax.
> Thanks,
> Bob Johnson
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Kai Zhuang
BioMedical Engineering @ University of Toronto
kai dot zhuang at gmail dot com

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