Hi,
at least for the binding free energy this sounds like a case for MM-PBSA.
If you want to try something more involved, you could try to do a
double-decoupling-TI calculation. For the former case, MM-PBSA is
explained in a tutorial on the Amber website.
Kind Regards,
Thomas
On Tue, April 20, 2010 10:07 am, George Tzotzos wrote:
> Hi everybody,
>
> I'm trying to work out the binding energy of a ligand/receptor complex as
> well as the actual contacts (hbonds) that the ligand makes with residues
> at the binding site. The ligand is around 15-25 atoms and the protein has
> 125 residues.
>
> Does anyone have a MD protocol for this type of work?
>
> Your help would be greatly appreciated
>
> George
>
>
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>
Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Tue Apr 20 2010 - 07:30:05 PDT
