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
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