[AMBER] folding RNA using SGLD

From: Asmita Gupta <asmita4des.gmail.com>
Date: Tue, 30 Jun 2015 19:41:21 +0530

Dear users,

  I am trying to study folding pathway of an RNA chain. Starting from an
extended conformation, the chain should adopt a pseudoknot structure. I
don't expect that the structure should ultimately fold into its native

Is self-guided langevin dynamics is a good idea to study this kind of
process. There are studies using Temperature replica exchange, but as far
as i have read, it involves reweighing to get canonical ensemble, while
this issue is not there with SGLD.

Please suggest n appropriate method as i couldn't find anything in the
literature using SGLD for RNA folding.


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Received on Tue Jun 30 2015 - 07:30:03 PDT
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