This sounds like an application of decomposition analysis. It's described
in the manual (MM/PBSA sections).
Good luck!
Jason
On Thu, Nov 4, 2010 at 11:54 AM, John S <s.john634.gmail.com> wrote:
> Dear Amber Users ,
>
> As I understood from the manual on MMPBSA as tool to calculate the MM
> binding energy , we need the vacuum topology files of ligand and receptor.
> Now if I need to calculate the binding energy contribution due to one chain
> of a molecule A with another chain of molecule B,(with chains as part of
> the
> molecule).
>
> Do I need to make a vacuum topology file of each chain separately .Is there
> any other way to obtain the contribution of each chain.
>
> Thanks
> John
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Nov 04 2010 - 09:32:16 PDT
