[gmx-users] changing atom types versus adding dihedrals to atom types

[Rafael I. Silverman y de la Vega]

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 <
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
>>> 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 at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu>| (410)
>> 706-7441
>>
>> ==============================**====================
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>
>