[gmx-users] About the biotin parameter.....

[Justin Lemkul]

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

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

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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