try the biotin/streptavidin one, at least for building the complex.
you might not want to use the water cap (use a full box).
> 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
> <mailto: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
>
>
> -----------------------------------------------------------------------
>
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu <mailto:amber.scripps.edu>
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> <mailto:majordomo.scripps.edu>
>
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Thu Feb 02 2006 - 06:10:06 PST
