[gmx-users] Re: Folding rate

[KS Rotondi]

Dear Bharat,

20 residue peptides in general don't fold, they inhabit a  
conformational space. Can you determine the fraction of time spent in  
a near native (as defined by you) conformation under given conditions  
to within the ability of the force field, yes, you can. To calculate a  
true rate of folding, if you were studying, say, the trp cage protein  
(20 AA, defined tertiary structure), you'd have to start with a  
primarily beta or helix chain (use a primary sequence secondary  
structure predictor to assign starting conformations) as would be  
expected to emerge from the ribosome, simulate until a native-like  
conformation was formed, and repeat many times until a statistically  
reasonable answer was approached, and even then, for something that  
small, I'd bet it spends a fair amount of time in non-native  
conformations.

Many times.

Ken

Dr. K.S. Rotondi
Departments of Chemistry, Biochemistry and Molecular Biology
The University of Massachusetts - Amherst
Amherst, MA 01003

"If there's a solution, why worry?, If there's no solution, why worry?"
	His Holiness, the Dalai Llama



On Dec 30, 2011, at 5:39 PM, bharat gupta wrote:

> Hi,
>
> I want to know whether it's possible to calculate the folding rate  
> of 20 residue peptide folding into a beta-hairpin using gromacs ??
>
> -- 
> Bharat
>
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