Thank's,
I am studying the complexation of four molecules (host:guest) in a solvated system. I want to count the number of hydrogen bond versus time (inter, intra and with water of my four molecule) using VMD. As water molecules are outside of the primary box, I thought it necessary to do reimage.
> Date: Thu, 27 Oct 2011 10:15:47 -0400
> From: daniel.r.roe.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] molecule out box and correct hbond analysis
>
> Hi,
>
> Currently the hbond routine does not use imaging. Ideally you would
> use the center and imaging commands to reorient your molecules of
> interest so that imaging is not a factor prior to using the hbond
> command. Can you please post a little more information about your
> system and how you tried to re-image it?
>
> -Dan
>
> On Thu, Oct 27, 2011 at 4:27 AM, mirage . <m.o.m.live.fr> wrote:
> >
> >
> > Hi Amber users,
> >
> > i am using different option to reimag my molecules but in some case a part of one molecule is out box ? How to do a correct hbound analysis in this caseThanks
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>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Postdoctoral Associate
> BioMaPS Institute, Rutgers University
> 610 Taylor Road
> Piscataway, NJ 08854
>
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Received on Thu Oct 27 2011 - 09:00:02 PDT
