Hi justin thank you for suggestion. I think to Calculate the free energy of solvation of biotin, I hve to use the method as per your tuotorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html Is these right or I have to do anything else??? With Best Wishes and regards, Rama david On Wed, Nov 28, 2012 at 6:03 PM, Justin Lemkul <[email protected]> wrote: > > > On 11/28/12 12:20 AM, rama david wrote: > >> Hi justin, >> >> Thank you for your suggestion. >> >> I read the ATB paper but the paper does not mention any thing related to >> the biotin. >> >> > Probably not, it's too complex to be considered a model compound. > > > When I mail them, they replied .. >> >> To clarify the validation: >> There are different levels of validation criteria used in the ATB. >> The one which is available on the ATB web-site for a given molecule is the >> validation of the topology against the compatibility with the GROMOS force >> field. The output contains energies for bonded parameters. >> The validation described in the paper is the validation against the >> experimental hydration free energy of small organic molecules. Biotin was >> not a part of the validation dataset. >> >> >> What should I have to do..??? >> > > Validation of a method (i.e., the ATB algorithm) and validation of the > resulting parameters are different concepts. It is still incumbent upon > you to demonstrate that the parameters you got from somewhere else (i.e., > ATB) are suitable for what you intend. If you were to manually derive the > parameters, you'd have to do the same thing. There is no guarantee that > any service (PRODRG, ATB, etc) are inherently correct. ATB is generally > quite good, but any reviewer worth his salt is going to ask whether or not > you have evidence that the biotin parameters you chose are actually going > to represent reality before you go spending a lot of time running > simulations, collecting data, and making conclusions. > > The underlying validation of Gromos96 parameters involves calculating free > energies of solvation for model compounds, which are then mapped back to > the desired molecule (usually some biomolecule like an amino acid). So, in > theory, you could: > > 1. Calculate the free energy of solvation of biotin, if it is known > 2. Run test simulations of biotin in your protein and verify that it > engages in known interactions > > Those are just what come to mind immediately, but you should consult the > literature for other cofactors and see how they were parameterized. > Gromos96 includes parameters for ATP, FAD, FMN, and others, so clearly > there is methodology somewhere to which you can refer. > > -Justin > > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- 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
