AMBER Archive (2006)

Subject: Re: AMBER: question capping helix ends

From: Vlad Cojocaru (
Date: Thu Mar 23 2006 - 04:48:14 CST

Are you doing explicit water simulations?? Are the last bp of the
helices Watson-Crick???

If yes, are you sure that the ends of your helices are flying apart ?...
My experience with RNA simulations in explicit water says that one
doesn't observe such behaviour if you have Watson-Crick bp at the end of
the helix (even with a helix containing only 3 G-Cs)... ...

If you really want, you may add some extra Watson-Crick bp ... 1-2 bp
wont make such a big difference...


Zhuang wrote:

>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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Dr. Vlad Cojocaru
EML Research gGmbH
Molecular and Cellular Modeling Group
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg, Germany
Phone: +49-6221-533266
Fax: +49-6221-533298

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