Dear Prof. Case,
Many thanks for your suggestion. I will go through Chimera as well
to do the needful.
Thanks and regards
Aditya.
On Wed, Feb 5, 2014 at 6:01 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> 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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--
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Aditya Kumar Padhi
Ph.D Scholar
School of Biological Sciences (SBS)
Indian Institute of Technology Delhi
New Delhi-110016, India
Contact no:+91-9711539958
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Received on Wed Feb 05 2014 - 07:00:04 PST
