Hi Ehud, we recently developed an extended amber99sb forcefield + some scripts which probably can do exactly what you want (setting up alchemical mutations for any amino acid mutation except for proline). We tested it by calculating thermostability differences for a set of 100+ mutations of an enzyme and got quite accurate agreement with experimental data (R=0.86 ). If you want I can send you the stuff you need to set up the simulations. Details about simulation parameters you can find in the paper. ( http://www.cell.com/biophysj/abstract/S0006-3495%2810%2900216-X )
In general I would not use a plain thermodynamic integration scheme because it does not converge very well, especially for large mutations. We used a Crooks-based non-equilibrium scheme which worked quite well but there are also other protocols around (multi-state BAR) which probably do equally well. -Daniel On Monday 05 July 2010 04:35:17 pm Ehud Schreiber wrote: > Dear GROMACS users, > > > > I am investigating a certain peptide which is well bound to some > protein; their configuration is known from the PDB. > > My aim is to compare the binding free energies of several variants of > the peptide. > > In particular, I wish to mutate some amino acids to others. > > I have read some tutorials and mailing list messages; still, I have > several questions unanswered. > > > > I plan to use the Thermodynamic Integration (TI) method in an > "alchemical" setting, in which I "turn off" the side chain. > > The "naked" amino acid will then be my reference point comparing to real > amino acids. > > In this way I should be able to obtain, using the usual thermodynamical > cycle, the binding free energy difference of two amino acids (Delta > Delta G), which is sufficient for my needs and should be more accurate > than computing absolute binding free energies (Delta G). > > > > 1) Does this sound like the best approach? > > 2) In particular, is it O.K. to use a "naked" amino acid (with no side > chain at all) as the reference, or should Glycine or Alanine be used? > > 3) Following the above procedure, I still would not achieve a "naked" > amino acid. > > Rather, a side chain "ghost" remains, non-interacting but still > bonded to itself and to the C-alpha. > Is it correct to assume that the contribution of such a "ghost" > would cancel between the free and bound peptide? > > 4) Are the OPLS-AA force field, theTIP-3P water model and the NpT > ensemble good choices? > > > > I have seen two methods used to make the change between the initial and > final states. > > The first (and simplest) is to use the couple-moltype parameter of > mdrun. > > However, this seems to change a whole molecule, while I'm interested in > changing only a part (the side chain). > > > > 5) Can I define the side chain and the amino acid backbone as different > molecules, and change the former, still connecting them one to the > other? > > > > Alternatively, the topology of the B state can be explicitly provided > (as described e.g. in section 5.7.4 of the version 4.0 user manual). > > > > 6) The atom charges can be specified for state B, as appropriate for > turning off the Coulomb interactions. > > In order to turn off the vdW ones, must I define new atom types? > > 7) Are there perhaps such amino acid variants already built? > > > > Finally, some technicalities: > > > > 8) I have seen the sc-alpha parameter (when sc-power = 1) given the > values 1.0, 0.7 and 0.5. What is recommended? > > 9) Should I employ DispCorr = EnerPres ? > > > > Thanks, > > Ehud Schreiber. > -- Dr. Daniel Seeliger Computational Biomolecular Dynamics Group Max-Planck-Institute for Biophysical Chemistry Tel. +49 (0) 551-201-2310 http://wwwuser.gwdg.de/~dseelig -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
