Sulpher is important, but it is in the apoprotein, not the parametrized prosthetic group
On Thu, Sep 19, 2013 at 6:51 PM, Rafael I. Silverman y de la Vega < rsilv...@ucsc.edu> wrote: > 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
