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

Ehud Schreiber schreib at compugen.co.il
Sun Oct 24 10:43:39 CEST 2010

Hi Moshen,

I think everybody agrees that a full calculation such as Free Energy
Perturbation is the accurate, if difficult and lengthy, approach.
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.



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
>> the Accelrys Discovery Studio.
>> Obviously, this is an approximation that might be too crude for some
>> applications.

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