[gmx-users] About the biotin parameter.....
ramadavidgroup at gmail.com
Wed Nov 28 14:08:21 CET 2012
Hi justin thank you for suggestion.
I think to Calculate the free energy of solvation of biotin, I hve to use
as per your tuotorial
Is these right or I have to do anything else???
With Best Wishes and regards,
On Wed, Nov 28, 2012 at 6:03 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 11/28/12 12:20 AM, rama david wrote:
>> Hi justin,
>> Thank you for your suggestion.
>> I read the ATB paper but the paper does not mention any thing related to
>> the biotin.
> Probably not, it's too complex to be considered a model compound.
> When I mail them, they replied ..
>> To clarify the validation:
>> There are different levels of validation criteria used in the ATB.
>> The one which is available on the ATB web-site for a given molecule is the
>> validation of the topology against the compatibility with the GROMOS force
>> field. The output contains energies for bonded parameters.
>> The validation described in the paper is the validation against the
>> experimental hydration free energy of small organic molecules. Biotin was
>> not a part of the validation dataset.
>> What should I have to do..???
> Validation of a method (i.e., the ATB algorithm) and validation of the
> resulting parameters are different concepts. It is still incumbent upon
> you to demonstrate that the parameters you got from somewhere else (i.e.,
> ATB) are suitable for what you intend. If you were to manually derive the
> parameters, you'd have to do the same thing. There is no guarantee that
> any service (PRODRG, ATB, etc) are inherently correct. ATB is generally
> quite good, but any reviewer worth his salt is going to ask whether or not
> you have evidence that the biotin parameters you chose are actually going
> to represent reality before you go spending a lot of time running
> simulations, collecting data, and making conclusions.
> The underlying validation of Gromos96 parameters involves calculating free
> energies of solvation for model compounds, which are then mapped back to
> the desired molecule (usually some biomolecule like an amino acid). So, in
> theory, you could:
> 1. Calculate the free energy of solvation of biotin, if it is known
> 2. Run test simulations of biotin in your protein and verify that it
> engages in known interactions
> Those are just what come to mind immediately, but you should consult the
> literature for other cofactors and see how they were parameterized.
> Gromos96 includes parameters for ATP, FAD, FMN, and others, so clearly
> there is methodology somewhere to which you can refer.
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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