Re: [AMBER] can we sample ligand conformation in Amber

From: Albert <mailmd2011.gmail.com>
Date: Sun, 26 Jun 2016 20:45:41 +0200

Hi guys, thanks for comments.

I just want to have alternative low energy conformation for docking. ...



On 06/26/2016 08:45 PM, Carlos Simmerling wrote:
> I think it's hard to help without knowing more. Is the ligand alone, or
> bound to something? very different problems. If bound, are you sampling
> conformations for internal degrees if freedom, or binding pose? Again very
> different. Lastly, how many degrees of freedom do you need to sample? Do
> you just need alternate conformations, or something about relative
> populations?


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Received on Sun Jun 26 2016 - 12:00:04 PDT
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