I am done with the tutorials and they are very helpful. With the help of
the these tut i am able to simulate my protein. But now I want to similate
my protein which has a ligand bound to it. As per
help in tut of simulating a pharmaceutical compound i am bale to generate
paprameters for my
ligand but how to add this ligand into original protein/ligand complex for
simulation. Is there any help
so that I can simulate my ligand bound protein.
thanks in advance.
snoze
On 2/1/06, Carlos Simmerling <carlos.simmerling.stonybrook.edu> wrote:
>
> I would suggest working through the tutorials on the Amber
> web site. Particularly useful may be the "protein with a nonstandard
> residue" and "simulating a pharmaceutical compound". Then read
> papers that use Amber to do the kind of thing that you want and
> check their methods section carefully.
>
>
> snoze pa wrote:
>
> > Hi, I am a new user in amber community. I want to simulate my protein
> > which has a ligand bound to it. This is a small
> > organic molecule bound to the active site in the protein. I want to
> > know how can i start my setup using this ligand and protein.
> > Any help from scratch will be higly appreciated.
> > thanks in advance.
> > snoze
>
>
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Received on Thu Feb 02 2006 - 06:10:06 PST
