AMBER Archive (2009)

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

From: Rilei Yu (
Date: Tue May 26 2009 - 19:21:15 CDT

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 <> 写道:

发件人: Carlos Simmerling <>
主题: Re: [AMBER] Molecular simulation of a protein using special H2O cluster
收件人: "AMBER Mailing List" <>
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 <> 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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