AMBER Archive (2006)

Subject: AMBER: question capping helix ends

From: Zhuang (ezhuang_at_chem.ucsb.edu)
Date: Thu Mar 23 2006 - 04:35:21 CST

Hi...I'm trying to simulate a RNA fragment that has helices. I'm
wondering if there is a method in sander to cap the helix end so that
they won't fly apart during the simulation. I know I can just add a
small loop to the helix end to provent that...but it's computationally
expensive to increase my system size by adding the loops. Is there a
way to solve the problem without increasing my system size? like
constrain the last residues on the helix to stay in watson-crick base
pair throughout the simulation? thanks
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