[gmx-users] about solvate

Rui Li moonfine at mail.sdu.edu.cn
Thu May 31 06:02:15 CEST 2007

yes,there are some water molecules embedded in an enzyme active site.If I remove
them,and use genbox to get new water molecules , Does it influence the simulation

>From: Mark Abraham <Mark.Abraham at anu.edu.au>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] about solvate
>Date:Thu, 31 May 2007 00:16:37 +1000
>Rui Li wrote:
> > Dear gmx-users:
> > 
> > I get a pdb file,and there are some water moleculers included in it. 
> >  Should I remove these water moleculers before I use genbox?
> Depends what those waters are doing. Waters embedded in an enzyme active 
> site should probably stay... but of course with such a system you would 
> have thought about the kind of thing you wanted to study before this, 
> right? :-) Waters in crystal packing sites can probably go or stay.
> What's the problem here?
> Mark
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