AMBER Archive (2006)

Subject: Re: AMBER: DNA helix end stable?

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Wed Nov 29 2006 - 06:24:14 CST

people have published articles on DNA simulations with implicit solvent,
have you read those? It's always good to read what others have done before
trying to analyze your data, especially if you're new to the project.
For example, check work by Tsui and Case.

a a wrote:

> Dear Sir/Madam,
>
> I am trying to do MD for DNA, I noted that the end of the DNA helix is
> very flexible (the double helix structure is lost too). Is it well
> known that double helix structure of DNA end will be unstable? I did
> the calculations with implicit solvent, but I found some other
> publications indicate the same observations when they used explicit
> solvent instead. Is it normal or just that I should change the
> conditions for the calculations to correct this problem?
>
> Best regards,
>
> Annie
>
> _________________________________________________________________
> No masks required! Use MSN Messenger to chat with friends and family.
> http://go.msnserver.com/HK/25382.asp
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu