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.
-Justin
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
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Justin A. Lemkul, Ph.D.
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Department of Pharmaceutical Sciences
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Health Sciences Facility II, Room 601
University of Maryland, Baltimore
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Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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