AMBER Archive (2005)

Subject: RE: AMBER: Leap handling crystallographic waters

From: Furse, Kristina Elisabet (kristina.e.furse_at_vanderbilt.edu)
Date: Tue Nov 22 2005 - 13:18:34 CST

I guess I was thinking of the "fast water routines"--is that no longer
operational in amber8?

Quoting Ross Walker <ross_at_rosswalker.co.uk>:

> 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
>
> /\
> \/
> |\oss Walker
>
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
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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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> >
>
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-----------------------------------------------------------------
Kristina E. Furse
Department of Chemistry
Center for Structural Biology
Vanderbilt University
Email: kristina.e.furse_at_Vanderbilt.Edu
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