[gmx-users] Re: DNA simulations

[Mark Abraham]

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.

>   Also,
> 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 
that. ;-)

Mark