Re: [AMBER] Request for MD protocol

From: <>
Date: Tue, 20 Apr 2010 10:14:31 -0400 (EDT)


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,


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
> _______________________________________________
> AMBER mailing list

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
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