On Wed, Feb 05, 2014, Aditya Padhi wrote:
> I want to place a protein molecule (appx. 20 kDa in size) into a
> viral capsid loop region which is about 7 amino acid long. What I want to
> do is to remove the 5 amino acids out from the loop region and place the 20
> kDa protein, so that the loop region can accommodate the 20 kDa protein. I
> am finding it difficult as the co-ordinates of both the molecules are
> different.
This is not really the sort of task that Amber is very good at. A modeling
program like Chimera might help you get close; after that, you could use Amber
to refine the initial structure.
...dac
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Received on Wed Feb 05 2014 - 05:00:02 PST
