AMBER Archive (2009)

Subject: Re: [AMBER] Molecular simulation of a protein using special H2O cluster

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue May 26 2009 - 06:45:50 CDT

you could try using the NMR distance restraints (nmropt=1). there are plenty
of examples in the archives of how to do this.

On Tue, May 26, 2009 at 4:20 AM, Rilei Yu <yulaomao1983_at_yahoo.com.cn> wrote:

> Dear AMBER users,
>
> Now, I am studying the conformation of a special protein in the speical
> solvent constituted by cyclic water hexamers. Now, my problem is that I
> cannot simulate such solvent. After all, the cyclic water hexamer is
> sustained by hydrogen bond that cannot exist in the normal condition. Can
> anyone provide me with an approach that can sustain the water
> clusters-cyclic water hexamers exsting in my system.
>
> I am really appreciated for your help!
>
> Best Regards,
>
> Rilei Yu
>
>
> ___________________________________________________________
> 好玩贺卡等你发，邮箱贺卡全新上线！
> http://card.mail.cn.yahoo.com/
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber