Hmm, I will have to do some more controls then, but I prob dont have time to do them till after quals this fall... You mention Hartree-Fock methods, does this mean that you disfavor DFT for some reason for this purpose?
On Tue, Sep 17, 2013 at 5:40 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/17/13 8:18 PM, Rafael I. Silverman y de la Vega wrote: > >> Can you give some examples of how these verifications are different for >> different force fields? It doesnt seem like verifying takes that much >> time, >> but a theorist prof in my department told me not to worry as long as my >> system doesnt blow up... >> > > IMHO simply not blowing up tells you nothing. I can show you a dozen > simulations that don't blow up that have terrible small molecule topologies > that produce bad results. > > Parametrization methods and validation procedures are defined in the > literature and one could easily fill a book chapter (or more) on such > topics, so I will not go into it in an email. You may have to go back > several years (or even decades) in the literature to get the full story. > > > And what do you mean "thourough parametrization? >> > > Most people hope for a simple, one-shot step they can take to parametrize > a small molecule. There are numerous "black box" methods out there, some > good and some bad. I advise people to be thorough in terms of what the > force field requires and what their chemical knowledge tells them. For > instance, for water interactions in CHARMM, HF/6-31G* works well for most > compounds, unless sulfur is involved, in which case we need to do a more > expensive MP2/6-31G* calculation. You can get an OK result for everything > with HF, but it's not sufficiently accurate in all cases. > > > I parametrized flavin mononucleotide using amber99sb-ildn, I used existing >> atomtypes in the force field, but I added partial atomic charges based on >> a >> decent DFT calculation in orca, and I had to add 2 distance restraints on >> the delta negatively charged phosphate oxygens to keep them from crashing >> into the delta positive hydrogen on the same phosphate. Is that thorough >> in >> your opinion? >> > > How does it compare with the results of running the molecule through > antechamber? Usually GAFF gives a reasonable topology with minimal > adjustment necessary. That's one of the benefits of Amber; there are very > well-defined protocols and a robust general force field for the > parametrization. > > -Justin > > > -- > ==============================**==================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalemkul@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu> | > (410) > 706-7441 > > ==============================**==================== > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<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
