Re: [AMBER] Query on introducing a protein

From: Aditya Padhi <adi.uoh.gmail.com>
Date: Wed, 5 Feb 2014 18:31:02 +0530

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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



-- 
********************************************
Aditya Kumar Padhi
Ph.D Scholar
School of Biological Sciences (SBS)
Indian Institute of Technology Delhi
New Delhi-110016, India
Contact no:+91-9711539958
********************************************
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Feb 05 2014 - 07:00:04 PST
Custom Search