[gmx-users] Energy estimations of the protein-ligand complexes

[James Starlight]

Mark,

I've told about estimation of the energy of the ligands compounds
(small hormone-like compounds) embedded in the receptors binding
pocket.

In other words I want to simulate that ligands in water as well as in
the receptor complex and compare it's potential energy values in both
cases. From such experiment I want to check hypothesis that in the
receptor interior the ligands always in more strained conformations (
with highter value of potential energy) than in the unbound state.

James

2012/12/4, Mark Abraham <mark.j.abraham at gmail.com>:
> What components will that potential energy have?
>
> Mark
>
> On Mon, Dec 3, 2012 at 6:54 PM, James Starlight
> <jmsstarlight at gmail.com>wrote:
>
>> Dear Gromacs Users!
>>
>> I'm simulating different complexes of the receptors with different
>> ligands.
>>
>> For each complex I want to determine potential energy (not the binding
>> energy) of the ligand molecule. In other words I want to check in what
>> exactly complex ligand was in more or less strained conformation due
>> to the binding pocket influence. How I could do such estimations ?
>>
>> Thanks for help
>>
>>
>> James
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