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

Rafael I. Silverman y de la Vega rsilverm at ucsc.edu
Fri Sep 20 03:51:21 CEST 2013

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