[gmx-users] Re: DNA simulations
Mark.Abraham at anu.edu.au
Thu Jul 5 02:42:11 CEST 2012
On 5/07/2012 12:28 AM, SatyaK wrote:
> Thanks Mark for your response. These are steps I followed to construct
> DNA+Water molecules.
> ----> editconf -f A.pdb -o A.gro -d 0.3
> ----> genbox -cp A.gro -cs -nice -20 -o A_water.gro
That's not going to achieve your objective. I gave you a workflow to do
it. You'll need to flesh out the details.
> I have not used any of the topology files (which I believed should be used
> in g_select)
No, they aren't.
> during the construction and I am not sure of handling it.
Hence the hints I gave about reading documentation... You're doing
something very specific and unique to your workflow. GROMACS tries hard
to make available tools to solve problems, but there cannot be a
one-step shrink-wrap solution for everything you could want to do.
> I ned to introduce some OH radicals also into the cylinder with some radius
> around the DNA. Could you guide me.
First, find a force field that parameterizes radicals. Good luck with
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