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

Justin A. Lemkul jalemkul at vt.edu
Sun Oct 24 14:18:09 CEST 2010

Ehud Schreiber wrote:
> Hi Moshen,
> I think everybody agrees that a full calculation such as Free Energy
> Perturbation is the accurate, if difficult and lengthy, approach.

Wouldn't convergence of such a system be a major issue with a method like FEP? 
I think PMF would be the better option here.  It would still require significant 
data collection, but I think it would be easier to get usable data.


> The entropic effects usually cannot simply be ignored. All I tried to
> say was that there are approximation schemes for these (see the
> reference below). Still, I would trust such approximations only when
> computing binding Delta Delta G between two close variants (e.g. a wild
> type protein and a one residue mutation) such that most entropic
> contributions would tend to cancel.
> Ehud. 
> ------------------------------
> Date: Thu, 21 Oct 2010 22:45:23 +0330
> From: mohsen ramezanpour <ramezanpour.mohsen at gmail.com>
> Subject: Re: [gmx-users] RE: Gibbs free energy of binding
>> 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.


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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