Do you have a structure for the bound conformation / orientation. If so,
do they spontaneously dissociate during MD?
It may be easier to start from the bound state rather than wait for a
spontaneous association event to occur during MD.
If you have a good guess at a bound conformation and they remain bound for
a reasonable duration, you can use MM-PBSA to estimate the free energy of
"binding" (association / dissociation).
How large are these ligands? Even if you don't have a bound structure
available, if they are relatively small you may be able to use docking
software / calculations (like autodock) to make a guess at their
associated / bound state.
-Wesley Botello-Smith
>> I have two different ligands that are co-administered to patients, I
>> want to learn about their mutual interaction or preferences in solution,
>> to see if we can say something about the best way to do so
>> (crystallization, nano-particles, etc.), so I did several simulations
>> using just two copies of the ligands in water, but they just seem to
>> escape each other during the simulation....
>>
>> I have actually three systems in one: A+A, A+B or B+B, A and B being the
>> two different molecules I have.
>
> Just a thought… How is your system built? Do you have ONE A + ONE B +
> Water? Or do you have multiple copies of A and B in solution?
>
> If the idea is to in study their mutual interaction, one thing could be to
> look at a box with multiple copies of each.
>
> Cheers,
> Gustavo.
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>
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Received on Fri Apr 25 2014 - 18:30:03 PDT
