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varsha Offline OP
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In the sampling of the conformations, it is observed that more number of structures have 310 helix in the place of alpha helix. What can be the reason for this kind of observation?

Thanks in advance for any comments/suggestions.

Varsha

Last edited by varsha; 12/10/12 08:24 AM.
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This is not the expected behavior; some possible explanations that come to mind are:
Your sequence may actually prefer the 3-10 conformation.
Your forcefield stabilizes the 3-10 conformation.
Your simulation setup (solvent, ions, cutoffs....) stabilizes the 3-10 conformation.
Your analysis is incorrect.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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