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

Wed Sep 18 02:18:50 CEST 2013

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...
And what do you mean "thourough parametrization?
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?
Thanks

On Thu, Sep 12, 2013 at 7:32 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/12/13 7:04 PM, Rafael I. Silverman y de la Vega wrote:
>
>> I see,
>>   when you say thorough parametrization and validation, what do you mean?
>> How does one validate the system, calculate free energy in solution and
>> compare it to tabulated data?
>>
>>
> The target data depend on the force field for which parameters are being
> developed.  Matching QM geometries, water interaction energies and
> distances, free energies of solvation, crystal structures, liquid
> properties, etc. are all useful depending on the underlying force field and
> how it was derived.  For bonded parameters, matching QM energy scans and/or
> vibrational properties are common.
>
> -Justin
>
>
>> On Wed, Sep 11, 2013 at 4:57 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 9/11/13 6:07 PM, Rafael I. Silverman y de la Vega wrote:
>>>
>>>  Hi all,
>>>> in another thread it was recommended that instead of changing the atom
>>>> types by analogy to ones with the desired parameter already assigned,
>>>> that
>>>> instead one should assign bonded parameters by analogy.  I was just
>>>> wondering how this is better?
>>>>
>>>>
>>> I didn't suggest that.  I said that any assignment by analogy can have
>>> negative outcomes.  Bonds and angles, in theory, are a bit easier to deal
>>> with because the nonbonded interactions between their atoms are excluded.
>>>   Torsions are very difficult because the torsional bonded terms have to
>>> be
>>> balanced against the charge and LJ parameters of atoms separated by 3
>>> bonds, i.e. 1-4 interactions.
>>>
>>> Let me state very clearly that, for any missing parameters, anything
>>> short
>>> of a thorough parametrization and validation is (in my purist mind)
>>> unsound.
>>>
>>>
>>>     As long as the atom type isnt too different, then why would the
>>> torsions
>>>
>>>> not work out right? If the parameters are interrelated, what makes it
>>>> better to add one term to an atom type rather than changing all the
>>>> terms
>>>> (to ones that are supposed to be together)?
>>>>
>>>>
>>>>  The key is being sufficiently similar, but even subtle differences
>>> between
>>> LJ parameters have very large consequences, especially for 1-4
>>> interactions, so I find it hard to believe that one will recapitulate
>>> accurate interactions in this case.  Of course, all assignments by
>>> analogy
>>> bear some penalty for nonequivalent groups.  I balked at your initial
>>> post
>>> in the other thread because there was no need to mess with atom types.
>>>  The
>>> system at hand there contained protein and lipid and could be completely
>>> described by existing atom types and bonded types, the OP there was just
>>> (and perhaps still is) constructing the force field incorrectly.  I felt
>>> it
>>> need to be stated that the approach there would not necessarily be
>>> productive, and to make sure the archive was complete so that no one
>>> would
>>> come across a post in vacuum and assume that he or she can simply swap
>>> around atom types to make error messages go away.  Your initial statement
>>> referred only to bonds and angles, which indeed would be insensitive to
>>> changes in LJ parameters on any of those atoms, but since the thread was
>>> in
>>> the context of dihedrals, I thought I should state my opinion there.
>>>
>>> -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 <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 <jalemkul at outerbanks.umaryland.edu> | (410)
> 706-7441
>
> ==============================**====================
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