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 - 19:25:03 CDT

I've never heard of anyone doing what you propose, so I think you need to
write some scripts to make the restraints.

On Tue, May 26, 2009 at 8:21 PM, Rilei Yu <yulaomao1983_at_yahoo.com.cn> wrote:

> Dear Dr. Carlos Simmerling,
>
> Thanks for your reply! I believe your suggestions is applicable, but you
> know it is really both time and energy consuming to restrain every clusters
> one by one. After all there will be thousands of clusters in my system.
>
> Furthermore, based on the archives, I find some cases that perform restaint
> on the protein rather than this cluster solvent. Can you give me more
> details please?
>
> Thanks in advance!
>
> Rilei Yu
>
> --- 09年5月26日，周二, Carlos Simmerling <carlos.simmerling_at_gmail.com> 写道：
>
>
> 发件人: Carlos Simmerling <carlos.simmerling_at_gmail.com>
> 主题: Re: [AMBER] Molecular simulation of a protein using special H2O cluster
> 收件人: "AMBER Mailing List" <amber_at_ambermd.org>
> 日期: 2009年5月26日,周二,下午7:45
>
>
> 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
> >
> >
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