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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