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

[Justin Lemkul]

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 <
> 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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>>
>>

-- 
==================================================

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 | (410) 706-7441

==================================================