[gmx-users] Position restraint file
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
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.
On 8/11/05, Bob Johnson <robertjo at physics.upenn.edu> wrote:
> 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.
> Bob Johnson
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BioMedical Engineering @ University of Toronto
kai dot zhuang at gmail dot com
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