Hello,
On Tue, Mar 9, 2010 at 1:37 PM, rui <ruisher.gmail.com> wrote:
> Hi, All,
>
> I need to calculate/minimize the energy for a protein ligand complex, the
> protein and the ligand is covalently bonded, is amber able to handle this
> problem? If so, can anyone suggest how to do it? Thanks.
A covalently bound "ligand" is treated no differently than any other
amino acid residue in a protein. The manual and tutorial page (
www.ambermd.org/tutorials ) give a good introduction on using Amber.
Good luck!
Jason
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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 Tue Mar 09 2010 - 11:30:06 PST
