On Sun, Feb 15, 2015, zahra khatti wrote:
> Dear amber usersI have one complex with two ligand and a receptor....
> How can I obtain binding free energy between two ligands
> and a receptor?
You can't use mm-pbsa tools in any simple way to do this. You really need to
sample the apo-protein, the system with either ligand1 or ligand 2 bound, and
the system with both ligands bound (for a total of 4 possible states). We
don't have any tools that automate this process.
Even for the simpler case of a single ligand, let me emphasize what is written
at the beginning of Chapter 29:
"None of these should be considered as a “black-box”, and users should be
familiar with Amber before attempting these sorts of calculations. These
scripts automate a series of calculations, and cannot trap all the types of
errors that might occur. You should be sure that you know how to carry out an
MM-PBSA calculation “by hand” (i.e., without using the scripts); if you don’t
understand in detail what is going on, you will have no good reason to trust
the results."
In the case of two ligands, you should use the "by hand" method. Please be
aware that MM-PBSA has many imperfections and limitations. Please think
carefully about what it is you hope to learn from the simulations before
embarking on a lot of calcualtions.
...good luck....dac
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Received on Sun Feb 15 2015 - 15:00:02 PST
