AMBER Archive (2004)

Subject: AMBER: LES methodology question

From: Vlad Cojocaru (
Date: Fri Feb 20 2004 - 06:12:14 CST

Dear Amber users,
   Iam simulating an RNA molecule using LES. My RNA has three
interesting subregions (2 helices and 1 loop) connected to eachother in
the order helix-loop-helix. I want to make LES subspace for all these
regions using 5 copies. Now ..there are 2 posibilities (or probably more):
1. Make 1 LES subspace and replace the entire region (~15 nucleotides)
with 5 copies of it
2. Make 1 LES subspace for the first helix (5 copies), another one (5
copies) for the loop and another one for the second helix (5 copies).

I would appreciate if somebody could comment on advantages and
disadvantages of each of these posibilies. More in general I would like
to have a discussion about 1 LES subspace of the region of interest
(more atoms copied) versus spliting the region of interest into more
than 1 LES subspace (more LES regions but les atoms copied per region)
Thank you very much

Vlad Cojocaru 
Max Planck Institute for Biophysical Chemistry 
Department: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1327 
home tel: ++49-551-9963204  

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