On Sat, 16 Apr 2016 12:04:02 +0530
Mary Varughese <maryvj1985.gmail.com> wrote:
> Sir,
>
> Is it possible to do absolute binding energy calculation for a ligand
> binding to a receptor using TI. Not relative binding energy but
> absolute. Could i do a transformation where the ligand disappear from
> the binding site of the receptor? (similar to solvation energy
> calculation where toluene disappear from the solvent)
>
> Also Is there any other method for that other than MMPBSA and TI.
Yes, you can do that. Technically there is no difference between
decoupling a small molecule from a solvent and the small molecule being
embedded in any other environment, except for the fact that you have to
deal with the end state in a heterogeneous environment like the
protein. Typically this is done with the help of carefully chosen
restraints. See
http://www.alchemistry.org/wiki/Example:_Absolute_Binding_Affinity and
http://www.alchemistry.org/wiki/GROMACS_4.6_example:_n-phenylglycinonitrile_binding_to_T4_lysozyme
(and references therein) for a well-defined protocol.
An alternative would be direct pulling with variants in equilibrium
(Umbrella Sampling) and non-equilibrium (Jarzynski/Crooks).
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Received on Sat Apr 16 2016 - 01:30:05 PDT
