[gmx-users] changing atom types versus adding dihedrals to atom types
jalemkul at vt.edu
Fri Sep 20 04:25:04 CEST 2013
On 9/19/13 9:51 PM, Rafael I. Silverman y de la Vega wrote:
> Sulpher is important, but it is in the apoprotein, not the parametrized
> prosthetic group
I only mentioned this as one example where user input and intuition is useful,
not necessarily to directly comment on anything you are doing.
> On Thu, Sep 19, 2013 at 6:51 PM, Rafael I. Silverman y de la Vega <
> rsilverm at 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 <jalemkul at 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
>>>> 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
>>>> 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
>>>> 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
>>> 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 at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu>| (410)
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Justin A. Lemkul, Ph.D.
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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