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.
Ehud. ------------------------------ Date: Thu, 21 Oct 2010 22:45:23 +0330 From: mohsen ramezanpour <[email protected]> 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 <[email protected]>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. >> > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
