Try this command (let's suppose each of your molecule has 10 residues, for
example):
trajin trajectory.dcd
center :1-10 mass
image origin center
center :1-20 mass
image center familiar
center :1-30ass
image center familiar
center :1-40mass
image center familiar
image familiar
hope this helps
On Thu, Oct 27, 2011 at 2:20 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> You should be able to center your 4 molecules and reimage all of your
> solvent around them, in which case your won't have to worry about
> imaging artifacts when using the hbond command. That assumes your box
> is large enough so that there is a decent amount of clearance between
> the molecules of interest and the box edge.
>
> -Dan
>
> On Thu, Oct 27, 2011 at 11:39 AM, mirage . <m.o.m.live.fr> wrote:
> >
> > 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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> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >>
> >>
> >>
> >> --
> >> -------------------------
> >> Daniel R. Roe, PhD
> >> Postdoctoral Associate
> >> BioMaPS Institute, Rutgers University
> >> 610 Taylor Road
> >> Piscataway, NJ 08854
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
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> >
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> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Postdoctoral Associate
> BioMaPS Institute, Rutgers University
> 610 Taylor Road
> Piscataway, NJ 08854
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
--
Bruno Barbosa Rodrigues
PhD Student - Physics Department
Universidade Federal de Minas Gerais - UFMG
Belo Horizonte - Brazil
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Received on Tue Nov 01 2011 - 05:00:09 PDT
