AMBER Archive (2005)

Subject: RE: AMBER: Leap handling crystallographic waters

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Nov 22 2005 - 11:46:38 CST

Note, in Amber 8 there is no difference between solute and solvent so it
will make no difference what the crystallographic waters are defined as. The
concept of separate solute and solvent dates back to the days when there
were separate thermostats for the two regions.

All the best
Ross

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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Furse, Kristina Elisabet
> Sent: Tuesday, November 22, 2005 09:14
> To: amber_at_scripps.edu
> Subject: Re: AMBER: Leap handling crystallographic waters
>
> If you want the crystallographic waters to be considered
> solute and not solvent
> for the actual simulation, I think you'll have to rename
> them--define a new
> residue with a name sander does not recognize as solvent. If
> you don't rename
> them, they'll get lumped in with the solvent leap adds.
>
> Kristina
>
> Quoting Andy Purkiss <a.purkiss_at_mail.cryst.bbk.ac.uk>:
>
> > solvateBox will leave the crystallographic water molecules
> in place and
> > solvate around then. Just load in the pdb file complete with the
> > crystallographic waters. Solvatebox applies to the unit you are
> > solvating and it doesn't care whether it is protein or
> water or both.
> >
> > On Tue, 2005-11-22 at 14:44 +0100, Vlad Cojocaru wrote:
> > > Dear Amber users,
> > > I have a question which might sound trivial but since
> I am using
> > > crystallograohic waters in the simulation for the first time, I am
> > > wondering how does solvateBox or solvateOct in Leap handle the
> > > crystallographic waters.
> > > I intend to keep all the crystallographic waters in
> my simulations
> > > so I would like to tell Leap that those waters are part of the
> > > "solute"...
> > >
> > > Best
> > > vlad
> > > --
> > >
> > > Dr. Vlad Cojocaru
> > > EML Research gGmbH
> > > Molecular and Cellular Modeling Group
> > > Villa Bosch
> > > Schloss-Wolfsbrunnenweg 33
> > > 69118 Heidelberg
> > > Germany
> > > Phone: +49-6221-533266
> > > Fax: +49-6221-533298
> > > e-mail: Vlad.Cojocaru_at_eml-r.villa-bosch.de
> > > Additional info: my home page
> > >
> > --
> > Cat, n.: Lapwarmer with built-in buzzer.
> >
> +-------------------------------------------------------------
> --------+
> > | Andy Purkiss, School of Crystallography, Birkbeck
> College, London |
> > | E-mail a.purkiss_at_mail.cryst.bbk.ac.uk
> |
> > | Phone 020 7631 6869 (Work) or 0776 490 360 (Mobile)
> |
> >
> +-------------------------------------------------------------
> --------+
> >
> >
> >
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>
>
> -----------------------------------------------------------------
> Kristina E. Furse
> Department of Chemistry
> Center for Structural Biology
> Vanderbilt University
> Email: kristina.e.furse_at_Vanderbilt.Edu
> --------------------------------------------------------------
> ---------
> The AMBER Mail Reflector
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