On Thu, Jun 09, 2011, Sindrila Dutta banik wrote:
>
> I want to study the dynamics of a enzyme complesed with the substrate
> molecules. In my case one of teh substrate molecule is ATP.
>
> The crystal structure contains the ATP but the residue name is as
> "HETATOM".
The residue name is a three character (at most) name in columns 18-20 of
the ATOM or HETATM record. The residue name is not "HETATM".
> But for ATP what is the residue template.
Please see
http://www.pharmacy.manchester.ac.uk/bryce/amber.
> I also want to add ion in a particular position. How to do this?
This question is hard to understand. By "ion" do you mean the ATP, or some
other ion? The ATP would automatically be placed where it is in the crystal
structure. If you want some other position, or some other ion, that would be
a model building or docking problem, which is ordinarily outside the scope
of the Amber suite of programs. But it may well be that I don't understand
what you want to do....
....dac
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Received on Thu Jun 09 2011 - 10:00:03 PDT
