Hi, Under constant pressure a potential energy change is in many cases a good approximation for the change of enthalpy (if only small variations of volume are present). However, for many biomolecular applications, and in particular ligand binding, the entropy contribution cannot be neglected unless you compare two very similar reactions (e.g., delta delta G of binding of two protein inhibitors with similar structures).
Examples on the size of T delta S are given in many publications discussing MM/PBSA and its variants - in the past we calculated absolute values that were in the same order of magnitude as delta G for a protein-peptide complex (http://dx.doi.org/10.1529/biophysj.106.085399). I'm not familiar with Material Studio, but there are several methods to calculate entropy changes from MD simulations - quasi harmonic analysis is one that's implemented in Gromacs and Wordom. All have their limitations, but the same is true for experimental measurements of entropy changes upon binding. Ran ------------------------------------------------ Ran Friedman Biträdande Lektor (Assistant Professor) Linnaeus University School of Natural Sciences 391 82 Kalmar, Sweden +46 480 44 6290 Telephone +46 76 207 8763 Mobile ran.fried...@lnu.se http://lnu.se/research-groups/computational-chemistry-and-biochemistry-group?l=en ------------------------------------------------ ________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Ehud Schreiber [schr...@compugen.co.il] Sent: 21 October 2010 10:39 To: gmx-users@gromacs.org Subject: [gmx-users] RE: Gibbs free energy of binding 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. 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? -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
