[gmx-users] RE: Gibbs free energy of binding

[mohsen ramezanpour]

reading your idea:
it seems to me I can't ignore entropy contribution because  my simulation is
at room tempreture.
Really I couldn't understand what can I do!
I am working at room tempreture and I want to estimate binding free
energy(delta G),can I ignore entropy in this simulation and calculate
binding free energy by the method that I said in my last email?
what do you think?
thank in advance for  your guid


On Thu, Oct 21, 2010 at 12:15 PM, David van der Spoel
<spoel at xray.bmc.uu.se>wrote:

> On 2010-10-21 10.39, Ehud Schreiber wrote:
>
>> Actually, I believe that using the energy difference, Delta E, as an
>> approximation to the free energy difference, Delta G, is a valid
>> approach (which I'm considering myself). The entropic contribution to
>> Delta G, namely -T Delta S, may be less prominent than Delta E.
>> In addition, Delta S can be approximated by various means - see e.g.
>> Doig&  Sternberg 1995. I understand that such an approach is utilized in
>> the Accelrys Discovery Studio.
>> Obviously, this is an approximation that might be too crude for some
>> applications.
>>
>
> As a simple example the hydrophobic effect at room temperature is largely
> due to the entropy of the water [ at high temp it is due to the enthalpy of
> the water ].
>
> Since the hydrophobic effect is involved in all ligand binding it seems
> quite hopeless to get any reliable numbers when neglecting entropy. No
> referee will buy that - I wouldn't.
>
>
>
>> What do you think?
>>
>> ------------------------------------------------------------------------
>> --
>>
>> On Oct 21, 2010, at 09:25 , Sander Pronk wrote:
>>
>> Hi Mohsen,
>>
>> The mean energy difference is only one component of the free energy
>> difference.
>>
>> Before you go any further I'd suggest reading a good book on molecular
>> simulations, like 'Understanding Molecular Simulations' by Frenkel and
>> Smit.
>>
>> There's a good reason free energy calculations cover over half of that
>> book.
>>
>> Sander
>>
>>
>> On Oct 21, 2010, at 09:18 , mohsen ramezanpour wrote:
>>
>>  Dear Justin
>>>
>>> If I do  two  MD simulations for a short time in the same
>>>
>> conditions(of course separately for protein and drug)
>>
>>>  and calculate total energy of each one and sum them with each other
>>>
>> as E1 as nonbonding free energy of system.
>>
>>> then a MD simulation for Protein-drug system in the same condition and
>>>
>> calculate it's total energy too as E2 as bound system .
>>
>>> what does (E1-E2)mean?
>>> I think it is binding free energy,Is not it?
>>> in the other hand when we are working on NPT ensamble it means Gibbs
>>>
>> free energy is the main energy and our total energy is equal to Gibbs
>> free energy.
>>
>>> Then,what is the problem?
>>>
>>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
>
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